Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water

Trivial trajectory parallelization of multicanonical molecular dynamics (TTP-McMD) explores the conformational space of a biological system with multiple short runs of McMD starting from various initial structures. This method simply connects (i.e., trivially parallelizes) the short trajectories and generates a long trajectory. First, we theoretically prove that the simple trajectory connection satisfies a detailed balance automatically. Thus, the resultant long trajectory is regarded as a single multicanonical trajectory. Second, we applied TTP-McMD to an alanine decapeptide with an all-atom model in explicit water to compute a free-energy landscape. The theory imposes two requirements on the multiple trajectories. We have demonstrated that TTP-McMD naturally satisfies the requirements. The TTP-McMD produces the free-energy landscape considerably faster than a single-run McMD does. We quantitatively showed that the accuracy of the computed landscape increases with increasing the number of multiple runs. Generally, the free-energy landscape of a large biological system is unknown a priori. The current method is suitable for conformational sampling of such a large system to reduce the waiting time to obtain a canonical ensemble statistically reliable.     

Consistent Burgers equation expansion method and its applications to high- dimensional Burgers-type equations

In this paper, a novel method, named the consistent Burgers equation expansion (CBEE) method, is proposed to solve nonlinear evolution equations (NLEEs) by the celebrated Burgers equation. NLEEs are said to be CBEE solvable if they are satisfied by the CBEE method. In order to verify the effectiveness of the CBEE method, we take (2+1)-dimensional Burgers equation as an example. From the (1+1)-dimensional Burgers equation, many new explicit solutions of the (2+1)-dimensional Burgers equation are derived. The obtained results illustrate that this method can be effectively extended to other NLEEs.     

Group Analysis,Fractional Explicit Solutions and Conservation Laws of Time Fractional Generalized Burgers Equation

The generalized fractional Burgers equation is studied in this paper. Using the classical Lie symmetry method, all of the vector fields and symmetry reduction of the equation with nonlinearity are constructed. In particular,an exact solution is provided by using the ansatz method. In addition, other types of exact solution are obtained via the invariant subspace method. Finally, conservation laws for this equation are derived.     

VARIATIONS ON A THEME BY EULER

1.IntroductionAHallliltolliansystemofdifferentialequationsonRZnisgivedbyP~~H,(P,q),q=HP(P,q),(1)wherep=(pl,'.,P.),q=(ql,',q.)eR"arethegeneralizedcoordinatesandmolllentarespectivelyandH(P,q)istheellergyofthesystem.Thesystem(1)canberewrittenasthecompactf…     

An immersed boundary vector potential-vorticity meshless solver of the incompressible Navier–Stokes equation

We present a strong form meshless solver for numerical solution of the nonstationary, incompressible, viscous Navier–Stokes equations in two (2D) and three dimensions (3D). We solve the flow equations in their stream function-vorticity (in 2D) and vector potential-vorticity (in 3D) formulation, by extending to 3D flows the boundary condition-enforced immersed boundary method, originally introduced in the literature for 2D problems. We use a Cartesian grid, uniform or locally refined, to discretize the spatial domain. We apply an explicit time integration scheme to update the transient vorticity equations, and we solve the Poisson type equation for the stream function or vector potential field using the meshless point collocation method. Spatial derivatives of the unknown field functions are computed using the discretization-corrected particle strength exchange method. We verify the accuracy of the proposed numerical scheme through commonly used benchmark and example problems. Excellent agreement with the data from the literature was achieved. The proposed method was shown to be very efficient, having relatively large critical time steps.     

p阶递推式的解公式之注

以文献[1]为基础，我们得到p阶循环方程式之解的一个间明公式，这不论是在理论上，还是实践方面，皆有一定的意义．