Related papers: Finding reaction pathways with optimal atomic inde…
Joint space trajectory optimization under end-effector task constraints leads to a challenging non-convex problem. Thus, a real-time adaptation of prior computed trajectories to perturbation in task constraints often becomes intractable.…
We introduce a powerful iterative algorithm to compute protein folding pathways, with realistic all-atom force fields. Using the path integral formalism, we explicitly derive a modified Langevin equation which samples directly the ensemble…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…
Spatio-temporal biochemical signaling in a large class of protein-protein interaction networks is well modeled by a reaction-diffusion system. The global existence of the solution to the reaction-diffusion system is determined by the…
Efficient synthesis recipes are needed both to streamline the manufacturing of complex materials and to accelerate the realization of theoretically predicted materials. Oftentimes the solid-state synthesis of multicomponent oxides is…
Simulating chemical reactions is a central challenge in computational chemistry, characterized by an uneven difficulty profile: while equilibrium reactant and product geometries are often classically tractable, intermediate transition…
Understanding how complex systems transition between states requires mapping the energy landscape that governs these changes. Local transition-state networks reveal the barrier architecture that explains observed behaviour and enables…
We describe a robust and efficient chain-of-states method for computing Minimum Energy Paths~(MEPs) associated to barrier-crossing events in poly-atomic systems. The path is parametrized in terms of a continuous variable $t \in [0,1]$ that…
Assessing whether a molecule can be synthesised is a primary task in drug discovery. It enables computational chemists to filter for viable compounds or bias molecular generative models. The notion of synthesisability is dynamic as it…
We examine most-likely paths between initial and final states for diffusive quantum trajectories in continuously monitored pure-state qubits, obtained as extrema of a stochastic path integral. We demonstrate the possibility of "multipaths"…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
We first derive the Hamilton-Jacobi theory underlying continuous-time Markov processes, and then use the construction to develop a variational algorithm for estimating escape (least improbable or first passage) paths for a generic…
The free energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path…
High-temperature reactions widely exist in nature. However, they are difficult to be characterized either experimentally or computationally. The routinely used minimum energy path (MEP) model in computational modeling of chemical reactions…
For predicting the kinetics of nucleic acid reactions, continuous-time Markov chains (CTMCs) are widely used. The rate of a reaction can be obtained through the mean first passage time (MFPT) of its CTMC. However, a typical issue in CTMCs…
Optimization of non-convex loss surfaces containing many local minima remains a critical problem in a variety of domains, including operations research, informatics, and material design. Yet, current techniques either require extremely high…
Power system restoration after a major blackout is a complex process, in which selection of energising paths is a key issue to realize unit and load restoration safely and efficiently. In general, the energising path scheme made beforehand…
A central problem of materials science is to determine whether a hypothetical material is stable without being synthesized, which is mathematically equivalent to a global optimization problem on a highly non-linear and multi-modal potential…
Hydrogen atom transfer (HAT) reactions are essential in many biological processes, such as radical migration in damaged proteins, but their mechanistic pathways remain incompletely understood. Simulating HAT is challenging due to the need…
In the dynamic field of materials science, the quest to find optimal structures with low potential energy is of great significance. Over the past two decades, the minima hopping algorithm has emerged as a successful tool in this pursuit. We…