Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Data loci in algebraic optimization

We consider parametric optimization problems from an algebraic viewpoint. The idea is to find all of the critical points of an objective function thereby determining a global optimum. For generic parameters (data) in the objective function the number of critical points remains constant. This number is known as the algebraic degree of an optimization problem. In this article, we go further by considering the inverse problem of finding parameters of the objective function so it gives rise to critical points exhibiting a special structure. For example if the critical point is in the singular locus, has some symmetry, or satisfies some other algebraic property. Our main result is a theorem describing such parameters.     

Extragradient and extrapolation methods with generalized Bregman distances for saddle point problems

In this paper, we introduce two Bregman-type algorithmic frameworks to generalize the extragradient and extrapolation methods. With the help of relative Lipschitzness and the Bregman distance tool, the iteration properties of the proposed frameworks are analyzed. As applied to smooth convex-concave saddle point problems, our theory rediscovers the main results in Mokhtari et al. (2020) [14] for wider frameworks under weaker assumptions via a conceptually different approach.     

Distance distributions and dynamics of a zinc finger peptide from fluorescence resonance energy transfer measurements

Time-resolved fluorescence resonance energy transfer (FRET) measurements were used to measure distance distributions and intramolecular dynamics (site-to-site diffusion) of a 28-residue single-domain zinc finger peptide in the absence and presence of zinc ion. Energy transfer was measured between TRP₁₄ and a N-terminal DNS group. As expected, the TRP-to-DNS distance distribution for zinc-bound peptide is shorter and narrower (R _av=11.2 Å,hw=2.8 Å) than the metal-free peptide (R _av=20.1 Å,hw=14.5 Å). The degree of mutual donor-to-acceptor diffusion (D) was also determined for these distributions. For zinc-bound peptide there is no detectible diffusion (D0.2 Ų/ns), whereas for metal-free peptide a considerable amount of motion is occurring between the donor and the acceptor (D=12 Ų/ns). These results indicate that the zinc-bound peptide folds into a unique, well-defined conformation, whereas the metal-free conformation is flexible and rapidly changing. The absence of detectible mutual site-to-site diffusion between the donor and the acceptor in the metal-bound zinc finger peptide indicates that intramolecular motion is essentially frozen out, on the FRET time scale, as a consequence of zinc coordination.Dedicated to the memory of Barbara D. Wells.     

ELASTIC BEHAVIOR OF PROTEIN-LIKE SINGLE CHAIN

The conformational properties and elastic behaviors of protein-like single chains in the process of tensile elongation were investigated by means of Monte Carlo method. The sequences of protein-like single chains contain two types of residues: hydrophobic (H) and hydrophilic (P). The average conformations and thermodynamics statistical properties of protein-like single chains with various elongation ratio λ were calculated. It was found that the mean-square end-to-end distance r increases with elongation ratio,λ. The tensor eigenvalues ratio of : decreases with elongation ratio λ for short (HP)x protein-like polymers, however, the ratio of : increases with elongation ratioλ,especially for long (H)x sequence. Average energy per bond increases with elongation ratioλ, especially for(H)x protein-like single chains. Helmholtz free energy per bond also increases with elongation ratioλ. Elastic force (f), energy contribution to force (fU) and entropy contribution to force (fs) for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.     

Influence of development distance on resolution in thin-layer chromatography

Theoretical equations are given to relate resolution with development distance. Comparative experiments undertaken with quaternary ammonium compounds as test substances and using a selection of basic drugs are presented. As expected, resolution decreases with shorter development distance. However, this effect is less pronounced for compounds with small R_f values and when the spot size at the starting point is kept small. It was also shown that, for correctly assessing resolution in relation to development distance, the amounts of material spotted have to be decreased for shorter development distances.     

Alpha-Beta Hybrid Quantum Associative Memory Using Hamming Distance

This work presents a quantum associative memory (Alpha-Beta HQAM) that uses the Hamming distance for pattern recovery. The proposal combines the Alpha-Beta associative memory, which reduces the dimensionality of patterns, with a quantum subroutine to calculate the Hamming distance in the recovery phase. Furthermore, patterns are initially stored in the memory as a quantum superposition in order to take advantage of its properties. Experiments testing the memory’s viability and performance were implemented using IBM’s Qiskit library.     

量子关联与原子间相互作用距离关系的研究

本文将两个二能级原子注入一个腔中,用共生纠缠的方法来度量两原子之间的纠缠并推出它们之间的量子失协,还给出了原子与环境之间的共生纠缠与量子失协的计算公式,讨论了原子自发衰变率的变化对量子纠缠及失协的影响,及不同的初始状态情况下,纠缠及失协随原子距离的演化情况。结果表明：原子自发衰变率减小,原子与环境之间的量子纠缠及失协增加;选择不同的初态,可以控制原子间出现纠缠死亡的现象或量子失协为零的状态。     

近红外光谱技术在鱼糜等级评定中的应用研究

利用近红外光谱技术,对冷冻和解冻状态的不同等级白姑鱼糜进行等级评定。采用一阶导数法和标准正态变量变换法进行光谱预处理,再对预处理后的数据进行主成分分析,以主成分分析-马氏距离模式识别方法建立不同等级白姑鱼糜的等级评定模型,并对7项理化指标(水分、蛋白质、粗脂肪、盐溶性蛋白、凝胶强度、持水率和白度值)进行了测定。结果表明,主成分分析可以将三个等级白姑鱼糜较好地区分开;冷冻状态白姑鱼糜建立的等级评定模型效果优于解冻状态白姑鱼糜,前者的综合预测正确率为96.3%,后者的综合预测正确率为83.3%;三个等级白姑鱼糜的理化指标存在一定的差异。研究表明,近红外光谱技术可以快速无损评定白姑鱼糜等级。     

基于复小波包分形理论的爬壁机器人故障检测

通过研究爬壁式机器人的控制和运动特征，提出一种基于复小波包分形理论的故障检测方法．利用复小波包的平移不变性，将爬壁式机器人传感器输出信号分解成独立的频谱，并进行阀值处理和重构，从而有效去除高频噪音并提取故障的特征频率；依据信号分形维数的多尺度不变性，在嵌入维数空间，采用维数最大距离法，确定复小波包域故障信号的关联雏数．仿真实验表明，爬壁式机器人在各种异常工作模式下的故障信号关联维数能比较真实地反映其故障状态空间，同时也验证了故障信号的关联维数低于正常信号的关联维数作为故障发生与否的定量判据的正确性．