Measure Upper Bounds for Nodal Sets of Eigenfunctions of the bi-Harmonic Operator

In this article, we consider eigenfunctions $u$ of the bi-harmonic operator, i.e., $\triangle^2u=\lambda^2u$ on $\Omega$ with some homogeneous linear boundary conditions. We assume that $\Omega\subseteq\mathbb{R}^n$ ($n\geq2$) is a $C^{\infty}$ bounded domain, $\partial\Omega$ is piecewise analytic and $\partial\Omega$ is analytic except a set $\Gamma\subseteq\partial\Omega$ which is a finite union of some compact $(n-2)$ dimensional submanifolds of $\partial\Omega$. The main result of this paper is that the measure upper bounds of the nodal sets of the eigenfunctions is controlled by $\sqrt{\lambda}$. We first define a frequency function and a doubling index related to these eigenfunctions. With the help of establishing the monotonicity formula, doubling conditions and various a priori estimates, we obtain that the $(n-1)$ dimensional Hausdorff measures of nodal sets of these eigenfunctions in a ball are controlled by the frequency function and $\sqrt{\lambda}$. In order to further control the frequency function with $\sqrt{\lambda}$, we first establish the relationship between the frequency function and the doubling index, and then separate the domain $\Omega$ into two parts: a domain away from $\Gamma$ and a domain near $\Gamma$, and develop iteration arguments to deal with the two cases respectively

Nonlinear backbone torsional pair correlations in proteins

Protein allostery requires dynamical structural correlations. Physical origin of which, however, remain elusive despite intensive studies during last two decades. Based on analysis of molecular dynamics (MD) simulation trajectories for ten proteins with different sizes and folds, we found that nonlinear backbone torsional pair (BTP) correlations, which are spatially more long-ranged and are mainly executed by loop residues, exist extensively in most analyzed proteins. Examination of torsional motion for correlated BTPs suggested that aharmonic torsional state transitions are essential for such non-linear correlations, which correspondingly occur on widely different and relatively longer time scales. In contrast, BTP correlations between backbone torsions in stable $\alpha$ helices and $\beta$ strands are mainly linear and spatially more short-ranged, and are more likely to associate with intra-well torsional dynamics. Further analysis revealed that the direct cause of non-linear contributions are heterogeneous, and in extreme cases canceling, linear correlations associated with different torsional states of participating torsions. Therefore, torsional state transitions of participating torsions for a correlated BTP are only necessary but not sufficient condition for significant non-linear contributions. These findings implicate a general search strategy for novel allosteric modulation of protein activities. Meanwhile, it was suggested that ensemble averaged correlation calculation and static contact network analysis, while insightful, are not sufficient to elucidate mechanisms underlying allosteric signal transmission in general, dynamical and time scale resolved analysis are essential.Comment: 25 pages, 8 figure

Shot Range and High Order Correlations in Proteins

The main chain dihedral angles play an important role to decide the protein conformation. The native states of a protein can be regard as an ensemble of a lot of similar conformations, in different conformations the main chain dihedral angles vary in a certain range. Each dihedral angle value can be described as a distribution, but only using the distribution can't describe the real conformation space. The reason is that the dihedral angle has correlation with others, especially the neighbor dihedral angles in primary sequence. In our study we analysis extensive molecular dynamics (MD) simulation trajectories of eleven proteins with different sizes and folds, we found that in stable second structure the correlations only exist between the dihedrals near to each other in primary sequence, long range correlations are rare. But in unstable structures (loop) long range correlations exist. Further we observed some characteristics of the short range correlations in different second structures ({\alpha}-helix, {\beta}-sheet) and we found that we can approximate good high order dihedral angle distribution good only use three order distribution in stable second structure which illustrates that high order correlations (over three order) is small in stable second structure

Critical points of solutions for mean curvature equation in strictly convex and nonconvex domains

In this paper, we mainly investigate the set of critical points associated to solutions of mean curvature equation with zero Dirichlet boundary condition in a strictly convex domain and a nonconvex domain respectively. Firstly, we deduce that mean curvature equation has exactly one nondegenerate critical point in a smooth, bounded and strictly convex domain of $\mathbb{R}^{n}(n\geq2)$. Secondly, we study the geometric structure about the critical set $K$ of solutions $u$ for the constant mean curvature equation in a concentric (respectively an eccentric) spherical annulus domain of $\mathbb{R}^{n}(n\geq3)$, and deduce that $K$ exists (respectively does not exist) a rotationally symmetric critical closed surface $S$. In fact, in an eccentric spherical annulus domain, $K$ is made up of finitely many isolated critical points ($p_1,p_2,\cdots,p_l$) on an axis and finitely many rotationally symmetric critical Jordan curves ($C_1,C_2,\cdots,C_k$) with respect to an axis.Comment: 13 pages, 5 figure

End-to-end driving simulation via angle branched network

Imitation learning for end-to-end autonomous driving has drawn attention from academic communities. Current methods either only use images as the input which is ambiguous when a car approaches an intersection, or use additional command information to navigate the vehicle but not automated enough. Focusing on making the vehicle drive along the given path, we propose a new navigation command that does not require human's participation and a novel model architecture called angle branched network. Both the new navigation command and the angle branched network are easy to understand and effective. Besides, we find that not only segmentation information but also depth information can boost the performance of the driving model. We conduct experiments in a 3D urban simulator and both qualitative and quantitative evaluation results show the effectiveness of our model.Comment: 10 pages,6 figure

Uniqueness of critical points of solutions to the mean curvature equation with Neumann and Robin boundary conditions

In this paper, we investigate the critical points of solutions to the prescribed constant mean curvature equation with Neumann and Robin boundary conditions respectively in a bounded smooth convex domain $\Omega$ of $\mathbb{R}^{n}(n\geq2)$. Firstly, we show the non-degeneracy and uniqueness of the critical points of solutions in a planar domain by using the local Chen & Huang's comparison technique and the geometric properties of approximate surfaces at the non-degenerate critical points. Secondly, we deduce the uniqueness and non-degeneracy of the critical points of solutions in a rotationally symmetric domain of $\mathbb{R}^{n}(n\geq3)$ by the projection of higher dimensional space onto two dimensional plane.Comment: 15pages, 4figure

Configurational space discretization and free energy calculation in complex molecular systems

Trajectories provide dynamical information that is discarded in free energy calculations, for which we sought to design a scheme with the hope of saving cost for generating dynamical information. We first demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Based on the thought that infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness, and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor, and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. These findings suggest that entropy enthalpy compensation is inherently a local phenomenon in configurational space. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy.Comment: 27 pages, 8 figures, 1 tabl

Stepwise quantum phonon pumping in plasmon-enhanced Raman scattering

Plasmon-enhanced Raman scattering (PERS) becomes nonlinear when phonon pumping and phonon-stimulated scattering come into play. It is fundamental to the understanding of PERS and its photobleaching behavior. By quantization of the molecular vibration coherent state into phonon number states, we theoretically predict a stepwise dependence of PERS intensity on laser power. Experimental evidence is presented by measuring a monolayer of malachite green isothiocyanate molecules sandwiched in individual gold nanosphere-plane antennas, under radially polarized laser excitation of sub-microWatt powers.Comment: 26 pages, 7 figure

Critical points of solutions to a quasilinear elliptic equation with nonhomogeneous Dirichlet boundary conditions

In this paper, we mainly investigate the critical points associated to solutions $u$ of a quasilinear elliptic equation with nonhomogeneous Dirichlet boundary conditions in a connected domain $\Omega$ in $\mathbb{R}^2$. Based on the fine analysis about the distribution of connected components of a super-level set $\{x\in \Omega: u(x)>t\}$ for any $\mathop {\min}_{\partial\Omega}u(x)<t<\mathop {\max}_{\partial\Omega}u(x)$, we obtain the geometric structure of interior critical points of $u$. Precisely, when $\Omega$ is simply connected, we develop a new method to prove $\Sigma_{i = 1}^k {{m_i}}+1=N$, where $m_1,\cdots,m_k$ are the respective multiplicities of interior critical points $x_1,\cdots,x_k$ of $u$ and $N$ is the number of global maximal points of $u$ on $\partial\Omega$. When $\Omega$ is an annular domain with the interior boundary $\gamma_I$ and the external boundary $\gamma_E$, where $u|_{\gamma_I}=H,~u|_{\gamma_E}=\psi(x)$ and $\psi(x)$ has $N$ local (global) maximal points on $\gamma_E$. For the case $\psi(x)\geq H$ or $\psi(x)\leq H$ or $\mathop {\min}\limits_{\gamma_E}\psi(x)<H<\mathop {\max}\limits_{\gamma_E}\psi(x)$, we show that $\Sigma_{i = 1}^k {{m_i}} \le N$ (either $\Sigma_{i = 1}^k {{m_i}}=N$ or $\Sigma_{i = 1}^k {{m_i}}+1=N$).Comment: 21pages, 13figure

An accelerated sharp-interface method for multiphase flows simulations

In this work, we develop an accelerated sharp-interface method based on (Hu et al., JCP, 2006) and (Luo et al., JCP, 2015) for multiphase flows simulations. Traditional multiphase simulation methods use the minimum time step of all fluids obtained according to CFL conditions to evolve the fluid states, which limits the computational efficiency, as the sound speed c of one fluid may be much larger than the others. To address this issue, based on the original GFM-like sharp interface methods, the present method is developed by solving the governing equations of each individual fluid with the corresponding time step. Without violating the numerical stability requirement, the states of fluid with larger time-scale features will be updated with a larger time step. The interaction step between two fluids is solved for synchronization, which is handled by interpolating the intermediate states of fluid with larger time-scale features. In addition, an interfacial flux correction is implemented to maintain the conservative property. The present method can be combined with a wavelet-based adaptive multi-resolution algorithm (Han et al., JCP, 2014) to achieve additional computational efficiency. A number of numerical tests indicate that the accuracy of the results obtained by the present method is comparable to the original costly method, with a significant speedup