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The interest in combining model-based control approaches with diffusion models has been growing. Although we have seen many impressive robotic control results in difficult tasks, the performance of diffusion models is highly sensitive to…
We present receptor hopping and receptor swapping free energy estimation protocols based on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands to two arbitrary receptors. The receptor hopping protocol,…
In this paper, we propose a variable time-step linear relaxation scheme for time-fractional phase-field equations with a free energy density in general polynomial form. The $L1^{+}$-CN formula is used to discretize the fractional…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
We consider a class of optimal power flow (OPF) applications where some loads offer a modulation service in exchange for an activation fee. These applications can be modeled as multi-period formulations of the OPF with discrete variables…
The Harmonic Balance-Alternating Frequency-Time domain (HB-AFT) method is extensively employed for dynamic response analysis of nonlinear systems. However, its application to high-dimensional complex systems is constrained by the manual…
A new method for implementing the kinetic energy operator for real-space, grid-based electronic structure codes is developed. It is based on multi-order Adaptive Finite Differencing (AFD) and uses atomic pseudo orbitals produced by the…
We propose a time-adaptive predictor/multi-corrector method to solve hyperbolic partial differential equations, based on the generalized-$\alpha$ scheme that provides user-control on the numerical dissipation and second-order accuracy in…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
From the onset of fundamental statistical mechanical constructs formulated in the late 19th century, alchemical free-energy methods slowly emerged and transitioned to become operational tools of biomolecular simulation applicable to a wide…
Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…
We introduce a robust optimization method for flip-free distortion energies used, for example, in parametrization, deformation, and volume correspondence. This method can minimize a variety of distortion energies, such as the symmetric…
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 address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
The backward differentiation formula (BDF) is a useful family of implicit methods for the numerical integration of stiff differential equations. It is well noticed that the stability and convergence of the $A$-stable BDF1 and BDF2 schemes…
We put forward a user-friendly framework of the truncated Wigner approximation (TWA) for dissipative quantum many-body systems. Our approach is computationally affordable and it features a straightforward implementation. The leverage of the…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…