Machine Learning Approaches for Metalloproteins

Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.     

Stochastic Theory of Discrete Binary Fragmentation—Kinetics and Thermodynamics

We formulate binary fragmentation as a discrete stochastic process in which an integer mass k splits into two integer fragments j, k−j, with rate proportional to the fragmentation kernel Fj,k−j. We construct the ensemble of all distributions that can form in fixed number of steps from initial mass M and obtain their probabilities in terms of the fragmentation kernel. We obtain its partition function, the mean distribution and its evolution in time, and determine its stability using standard thermodynamic tools. We show that shattering is a phase transition that takes place when the stability conditions of the partition function are violated. We further discuss the close analogy between shattering and gelation, and between fragmentation and aggregation in general.     

Geometric Integration Methods that Preserve Lyapunov Functions

We consider ordinary differential equations (ODEs) with a known Lyapunov function V. To ensure that a numerical integrator reflects the correct dynamical behaviour of the system, the numerical integrator should have V as a discrete Lyapunov function. Only second-order geometric integrators of this type are known for arbitrary Lyapunov functions. In this paper we describe projection-based methods of arbitrary order that preserve any given Lyapunov function. AMS subject classification (2000) 65L05, 65L06, 65L20, 65P40     

Global Stability Results for the Weak Vector Variational Inequality

In this paper, we consider the global stability of solutions of a Weak Vector Variational Inequality in a finite-dimensional Euclidean space. Upper semi-continuity of the solution set mapping is established. And by a scalarization method, we derive a sufficient condition that guarantees the lower semi-continuity of the solution set mapping for the Weak Vector Variational Inequality     

Nonnormality and stochastic differential equations

A highly nonnormal Jacobian may give rise to large transients. This behaviour has been shown to have implications for (a) the relevance of linearising a nonlinear system and (b) the timestep restrictions required to keep a numerical method stable. Here, we show that nonnormality also manifests itself for stochastic differential equations. We give an example of a family of systems that is stable without noise, but can be made exponentially unstable in mean-square by a noise perturbation that shrinks to zero as the nonnormality increases. We then show via finite-time convergence theory that an Euler approximation shares the same property, giving a discrete analogue of the result. In memory of Germund Dahlquist (1925–2005).AMS subject classification (2000) 65C30, 34F05     

关于一类四阶非线性系统李雅普诺夫函数构造的研究

本文导出了四维线性系统的李雅普诺夫函数公式,研究了一类四阶非线性系统平凡解的稳定性。     

稀土X (X=La、Ce、Pr、Nd)修饰单层h-MoS2的NO气敏性

为提高h-MoS₂对NO的气敏性,采用第一性原理研究了X(X=La、Ce、Pr和Nd)对h-MoS₂的稳定性、吸附特性、功函数和伏安特性的影响.研究结果表明：X(X=La、Ce、Pr和Nd)取代Mo原子后得到的形成能均为负,说明掺杂体系容易形成且稳定存在.同时X掺杂后的h-MoS₂布居数相比于未掺杂前的大,也说明掺杂有利于体系稳定.NO吸附在La、Ce原子顶部位置的吸附能为-1.215 eV、-1.225 eV,吸附距离分别为2.475?、2.854?,具有明显的化学吸附特征.同时Hirshfeld转移电荷分别为0.213e和0.325e,具有明显的受体特征,提高了气敏性.La和Ce掺杂后能明显改变功函数的大小,也说明La和Ce能提高h-MoS₂对NO的气敏性.施加电场后能有效提高Pr掺杂体系的吸附强度,增大Hirshfeld转移电荷,对功函数的改变最大,所以电场对Pr掺杂体系的影响非常明显.通过分析掺杂体系的伏安特性曲线,La、Ce两掺杂体系的电流分别由0增大到5.3μA和4.8μA,而Pr、Nd...     

C_2^+ (X^4 Σ_g^-,1^4 Σ_u^+)离子体系解析势能函数、光谱常数和振动能级研究

采用多参考组态相互作用(MRCI)方法,结合aug-cc-pV6Z(AV6Z)基组,计算了C₂⁺(X⁴Σ_g^-,1⁴Σ_u⁺)的势能曲线,计算过程中考虑了Davidson修正和相对论效应,并将结果外推至完备基组(CBS)的极限.基于得到的单点能量,用最小二乘法方法进行了Murrell-Sorbie函数拟合,得到了势能函数解析式(APEF).基于APEF,计算了C₂⁺(X⁴Σ_g^-,1⁴Σ_u⁺)离子体系的离解能D_e,平衡核间距R_e,光谱常数ω_e,ω_eχ_e,B_e,α_e,结果与实验和其他理论计算值符合...