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.     

A public-key cryptosystem utilizing cyclotomic fields

While it is well-known that the RSA public-key cryptosystem can be broken if its modulusN can be factored, it is not known whether there are other ways of breaking RSA. This paper presents a public-key scheme which necessarily requires knowledge of the factorization of its modulus in order to be broken. Rabin introduced the first system whose security is equivalent to the difficulty of factoring the modulus. His scheme is based on squaring (cubing) for encryption and extracting square (cube) roots for decryption. This introduces a 14 (19) ambiguity in the decryption. Various schemes which overcome this problem have been introduced for both the quadratic and cubic case. We generalize the ideas of Williams' cubic system to larger prime exponents. The cases of higher prime order introduce a number of problems not encountered in the quadratic and cubic cases, namely the existence of fundamental units in the underlying cyclotomic field, the evaluation of higher power residue symbols, and the increased difficulty of Euclidean division in the field.     

Gaussian,non-Gaussian critical fluctuations in the Curie-Weiss model

It is known that at the critical temperature the Curie-Weiss mean-field model has non-Gaussian fluctuations and that internal fluctuations can be Gaussian. Here we compute the distribution of theq-mode magnetization fluctuations as a function of the temperature, the wave vectorq, and a fading out external field. We obtain new classes of probability distributions generated by this external field as well as new critical behavior in terms of its rate of fading out. We discuss also the susceptibility as the limitq tending to zero.     

On quadratic forms of height two and a theorem of Wadsworth

Let and be anisotropic quadratic forms over a field of characteristic not . Their function fields and are said to be equivalent (over ) if and are isotropic. We consider the case where and is divisible by an -fold Pfister form. We determine those forms for which becomes isotropic over if , and provide partial results for . These results imply that if and are equivalent and , then is similar to over . This together with already known results yields that if is of height and degree or , and if , then and are equivalent iff and are isomorphic over .

     

On the mechanism of proton transfer in imidazole

The force fields, in-plane vibrations, and relative intensities of Raman spectra have been calculated and analyzed for the N₁H and N₃H tautomers of imidazole, imidazolium cation, and their model structures. The results obtained for the isolated state of imidazole correspond to the intramolecular mechanism of proton transfer.     

Generation of Molecular Fields, Quantum Similarity Measures and Related Questions

A straightforward discussion on how to generate molecular fields is developed within the postulates of quantum mechanics. The theoretical formalism points towards the generalization and extension of the well-known molecular field forms, associated to density function and electrostatic molecular potential (EMP), including another category of fields associated to quantum molecular similarity measures. The results show that the new formalism can be easily applied to obtain an unlimited number of new information about molecular behavior.     

Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis

QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169-176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (approximately 16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 A) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product-reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute approximately 40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies.     

Microcalorimetry as a possible tool for phylogenetic studies of Tetrahymena

Using isothermal microcalorimetry, the growth power-time curves of three strains of Tetrahymena were determined at 28°C. Their Euclidean distances and cluster analysis diagram were obtained by using two thermokinetic parameters (r and Q_log), which showed that T. thermophila BF₁ and T. thermophila BF₅ had a closer relationship. Compared with the single molecular biomarker (ITS1) method, microcalorimetry wasmaybe a simpler, more sensitive andmore economic technique in the phylogenetic studies of Tetrahymena species.     

On the representation of electrostatic fields around ab initio charge distributions

Summary We compare two methods (Mulliken charges and a distributed multipole analysis, DMA) of representing an ab initio charge distribution for calculating the electrostatic field and potential outside the molecule, using pyrimidine and the RNA base uracil as examples. This is done using a 3-D graphical display of the electrostatic fields, which, when used with real-time rotation, zooming and clipping, has many advantages for qualitatively assessing the electrostatic interactions of a molecule. The errors involved in using Mulliken point charges may be of similar magnitude to the total electrostatic field in regions which are important in recognition processes. The DMA representation automatically includes the anisotropic electrostatic effects of non-spherical features in the charge distribution of each atom, and yet the displayed electrostatic fields around the atoms which have lone-pair density do not show marked anisotropy.