Ligand-receptor binding and unbinding are fundamental biomolecular processes and particularly essential to drug efficacy. Environmental water fluctuations, however, impact the corresponding thermodynamics and kinetics and thereby challenge theoretical descriptions. Here, we devise a holistic, implicit-solvent, multi-method approach to predict the (un)binding kinetics for a generic ligand-pocket model. We use the variational implicit-solvent model (VISM) to calculate the solute-solvent interfacial structures and the corresponding free energies, and combine the VISM with the string method to obtain the minimum energy paths and transition states between the various metastable (“dry” and “wet”) hydration states. The resulting dry-wet transition rates are then used in a spatially-dependent multi-state continuous-time Markov chain Brownian dynamics simulations, and the related Fokker–Planck equation calculations, of the ligand stochastic motion, providing the mean first-passage times for binding and unbinding. We find the hydration transitions to significantly slow down the binding process, in semi-quantitative agreement with existing explicit-water simulations, but significantly accelerate the unbinding process. Moreover, our methods allow the characterization of non-equilibrium hydration states of pocket and ligand during the ligand movement, for which we find substantial memory and hysteresis effects for binding versus unbinding. Our study thus provides a significant step forward towards efficient, physics-based interpretation and predictions of the complex kinetics in realistic ligand-receptor systems.

We propose a numerically efficient algorithm for simulating the multi-color optical self-focusing phenomena in nematic liquid crystals. The propagation of the nematicon is modeled by a parabolic wave equation coupled with a nonlinear elliptic partial differential equation governing the angle between the crystal and the direction of propagation. Numerically, the paraxial parabolic wave equation is solved by a fast Huygens sweeping method, while the nonlinear elliptic PDE is handled by the alternating direction explicit (ADE) method. The overall algorithm is shown to be numerically efficient for computing high frequency beam propagations.

A variety of problems in computational physics and engineering require the convolu- tion of the heat kernel (a Gaussian) with either discrete sources, densities supported on boundaries, or continuous volume distributions. We present a unified fast Gauss transform for this purpose in two dimensions, making use of an adaptive quad-tree discretization on a unit square which is assumed to contain all sources. Our implementation permits either free-space or periodic boundary conditions to be imposed, and is efficient for any choice of variance in the Gaussian.

he incompressibility constraint makes Navier-Stokes equations difficult. A reformulation to a better posed problem is needed before solving it numerically. The sequential regularization method (SRM) is a reformulation which combines the penalty method with a stabilization method in the context of constrained dynamical systems and has the benefit of both methods. In the paper, we study the existence and uniqueness for the solution of the SRM and provide a simple proof of the convergence of the solution of the SRM to the solution of the Navier-Stokes equations. We also give error estimates for the time discretized SRM formulation.

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