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     

Resistance distance and Laplacian spectrum

The resistance distance r _ij between two vertices v _i and v _j of a (connected, molecular) graph G is equal to the resistance between the respective two points of an electrical network, constructed so as to correspond to G, such that the resistance of any two adjacent points is unity. We show how the matrix elements r _ij can be expressed in terms of the Laplacian eigenvalues and eigenvectors of G. In addition, we determine certain properties of the resistance matrix R=||r _ij ||. AcknowledgementsThis research was supported by the Natural Science Foundation of China and Fujian Province, and by the Ministry of Sciences, Technologies and Development of Serbia, within Project no. 1389. The authors thank Douglas J. Klein (Galveston) for useful comments.     

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.     

一类联图的距离谱半径以及盖理论（英文）

令X=(n₁,n₂,…,n_t),Y=(m₁,m₂,…,m_t)是两个t维递减序列.如果对所有的j,1≤j≤t,都有∑_i=1~j、n_i≥∑_i=1~j m_i以及∑_i=1~t n_i=∑_i=1~t m_i,则称X可盖Y,记作X■Y.如果X≠Y,则记作X■Y.本文考虑联图G(n₁,n₂,…,n_t;a)=(K_n1∪_n2∪…∪K_nt)∨K_a的谱半径,这里n₁+n₂+…+n_t+a=n,(n₁,n     

Besov spaces and the multifractal hypothesis

Parisi and Frisch proposed some time ago an explanation for multiscaling of turbulent velocity structure functions in terms of a multifractal hypothesis, i.e., they conjecture that the velocity field has local Hölder exponents in a range [h _min,h _max], with exponents <h occurring on a setS(h) with a fractal dimensionD(h). Heuristic reasoning led them to an expression for the scaling exponentz _p ofpth order as the Legendre transform of the codimensiond-D(h). We show here that a part of the multifractal hypothesis is correct under even weaker assumptions: namely, if the velocity field hasL ^p -mean Hölder indexs, i.e., if it lies in the Besov spaceB _p ^s, , then local Hölder regularity is satisfied. Ifs<d/p, then the hypothesis is true in a generalized sense of Hölder space with negative exponents and we discuss the proper definition of local Hölder classes of negative index. Finally, if a certain box-counting dimension exists, then the Legendre transform of its codimension gives the scaling exponentz _p , and, more generally, the maximal Besov index of order,p, ass _p =z _p /p. Our method of proof is derived from a recent paper of S. Jaffard using compactly-supported, orthonormal wavelet bases and gives an extension of his results. We discuss implications of the theorems for ensemble-average scaling and fluid turbulence.     

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.     

Thermal analysis and X-ray studies of chiral ferroelectric liquid crystalline materials and their binary mixtures

Summary Thermal properties of a homologous series of ferroelectric liquid crystals S-(-)-[4-(2-n-alkoxy-propionyloxy)]biphenyl-4'-[n-alkoxy-(3,5-dimethyl)]benzoate have been investigated by polarizing optical microscopy and differential scanning calorimetry. The mesophases were identified and confirmed by X-ray too. Three binary mixtures were prepared from the individual homologues. In one of the mixtures (Mix1), the ferroelectric SmC* phase has broadened and became enantiotropic. This mesophase remained monotropic in the other two mixtures (Mix2, Mix3). The chiral nematic N* phase did not appear in Mix1, but remained monotropic for the other two mixtures. Two molecular parameters, the layer spacing and the average intermolecular distance have been calculated from the X-ray results for the homologues and their mixtures. An intercalated tail-to-tail packing of molecules was found both in the single compounds and their mixtures resulting in the layer spacing about half of the molecular length of the single compounds.     

Properties of the skeleton of aggregates grown on a Cayley tree

We discuss and analyze a family of trees grown on a Cayley tree, that allows for a variable exponent in the expression for the mass as a function of chemical distance, M(l)l ^dl . For the suggested model, the corresponding exponent for the mass of the skeleton,d _l ^s , can be expressed in terms ofd _l asd _l ^s = 1,d _l d _l ^c = 2;d _l ^s = d _l –1,d ₁ d _l ^c = 2, which implies that the tree is finitely ramified ford _l 2 and infinitely ramified whend _l 2. Our results are derived using a recursion relation that takes advantage of the one-dimensional nature of the problem. We also present results for the diffusion exponents and probability of return to the origin of a random walk on these trees.     

三级相互作用对聚亚甲基链末端距四次矩的影响

本文用三级相互作用近似理论导出了高分子链末端距的四次矩的计算公式。计算聚亚甲基链的末端距四次矩,并同二级相互作用的结果进行了比较。对于聚亚甲基链,三级相互作用近似的四次矩小于二级相互作用近似的四次矩。