The hydrodynamic limit for the Boltzmann equation is studied in the case when the limit system, that is, the system of Euler equations contains contact discontinuities. When suitable initial data is chosen to avoid the initial layer, we prove that there exist a family of solutions to the Boltzmann equation globally in time for small Knudsen number. And this family of solutions converge to the local Maxwellian defined by the contact discontinuity of the Euler equations uniformly away from the discontinuity as the Knudsen number <i></i> tends to zero. The proof is obtained by an appropriately chosen scaling and the energy method through the micro-macro decomposition.

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.

In recent years, great success has been achieved on the classification of symmetry-protected topological (SPT) phases for interacting fermion systems by using generalized cohomology theory. However, the explicit calculation of generalized cohomology theory is extremely hard due to the difficulty of computing obstruction functions. In this paper, based on the physical picture of topological invariants and mathematical techniques in homotopy algebra, we develop an algorithm to resolve this hard problem. It is well known that cochains in the cohomology of the symmetry group, which are used to enumerate the SPT phases, can be expressed equivalently in different linear bases, known as the resolutions. By expressing the cochains in a reduced resolution containing much fewer basis than the choice commonly used in previous studies, the computational cost is drastically reduced. In particular, it reduces the computational cost for infinite discrete symmetry groups, like the wallpaper groups and space groups, from infinity to finity. As examples, we compute the classification of two-dimensional interacting fermionic SPT phases, for all 17 wallpaper symmetry groups.

Thetransmissioneigenvalueproblem,besidesitscriticalroleininversescattering problems, deserves special interest of its own due to the fact that the corresponding differen- tial operator is neither elliptic nor self-adjoint. In this paper, we provide a spectral analysis and propose a novel iterative algorithm for the computation of a few positive real eigen- values and the corresponding eigenfunctions of the transmission eigenvalue problem. Based on approximation using continuous finite elements, we first derive an associated symmetric quadratic eigenvalue problem (QEP) for the transmission eigenvalue problem to eliminate the nonphysical zero eigenvalues while preserve all nonzero ones. In addition, the derived QEP enables us to consider more refined discretization to overcome the limitation on the number of degrees of freedom. We then transform the QEP to a parameterized symmet- ric definite generalized eigenvalue problem (GEP) and develop a secant-type iteration for solving the resulting GEPs. Moreover, we carry out spectral analysis for various existence intervals of desired positive real eigenvalues, since a few lowest positive real transmission eigenvalues are of practical interest in the estimation and the reconstruction of the index of refraction. Numerical experiments show that the proposed method can find those desired smallest positive real transmission eigenvalues accurately, efficiently, and robustly.

No abstract uploaded!