Showing papers by "University of Warsaw published in 1995"

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Abstract: We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use of a simple diagonal potential function and electrostatic potential fit atom centered charges. The need for a 10-12 function for representing hydrogen bonds is no longer necessary due to the improved performance of the new charge model and new van der Waals parameters. These new charges are determined using a 6-31G* basis set and restrained electrostatic potential (RESP) fitting and have been shown to reproduce interaction energies, free energies of solvation, and conformational energies of simple small molecules to a good degree of accuracy. Furthermore, the new RESP charges exhibit less variability as a function of the molecular conformation used in the charge determination. The new van der Waals parameters have been derived from liquid simulations and include hydrogen parameters which take into account the effects of any geminal electronegative atoms. The bonded parameters developed by Weiner et al. were modified as necessary to reproduce experimental vibrational frequencies and structures. Most of the simple dihedral parameters have been retained from Weiner et al., but a complex set of 4 and yj parameters which do a good job of reproducing the energies of the low-energy conformations of glycyl and alanyl dipeptides has been developed for the peptide backbone.

Quantization of diffeomorphism invariant theories of connections with local degrees of freedom

Abstract: Quantization of diffeomorphism invariant theories of connections is studied and the quantum diffeomorphism constraint is solved. The space of solutions is equipped with an inner product that is shown to satisfy the physical reality conditions. This provides, in particular, a quantization of the Husain–Kuchař model. The main results also pave the way to quantization of other diffeomorphism invariant theories such as general relativity. In the Riemannian case (i.e., signature ++++), the approach appears to contain all the necessary ingredients already. In the Lorentzian case, it will have to be combined in an appropriate fashion with a coherent state transform to incorporate complex connections.

Projective techniques and functional integration for gauge theories

Abstract: A general framework for integration over certain infinite dimensional spaces is first developed using projective limits of a projective family of compact Hausdorff spaces. The procedure is then applied to gauge theories to carry out integration over the non‐linear, infinite dimensional spaces of connections modulo gauge transformations. This method of evaluating functional integrals can be used either in the Euclidean path integral approach or the Lorentzian canonical approach. A number of measures discussed are diffeomorphism invariant and therefore of interest to (the connection dynamics version of) quantum general relativity. The account is pedagogical; in particular, prior knowledge of projective techniques is not assumed.

Symmetries of quantum spaces. subgroups and quotient spaces of quantum su(2) and so(3) groups

Abstract: We prove that each action of a compact matrix quantum group on a compact quantum space can be decomposed into irreducible representations of the group. We give the formula for the corresponding multiplicities in the case of the quotient quantum spaces. We describe the subgroups and the quotient spaces of quantumSU(2) andSO(3) groups.

Modelling the Galactic Bar Using Red Clump Stars

Abstract: The color-magnitude diagrams of $\sim 1 \times 10^6$ stars obtained for 19 fields towards the Galactic bulge with the OGLE project reveal a well-defined population of bulge red clump stars. We found that the distributions of the extinction-adjusted apparent magnitudes of red clump stars in fields lying at $l=\pm5°$ in galactic longitude differ by $\sim 0.4\; mag$. A plausible explanation of this observed difference in the luminosity distribution is that the Galactic bulge is a triaxial structure, or a bar, which is inclined to the line of sight by no more than $45°$. The part of the bar at the positive galactic longitude is closer to us. Work is now under way to model the Galactic bar by fitting the observed luminosity functions in the red clump region for various fields. Preliminary results indicate that the angle of the inclination of the bar to the line of sight can be as small as $\sim20°$. Gravitational microlensing can provide us with additional constrains on the structure of the Galactic bar.

High concentration of atmospheric 14 C during the Younger Dryas cold episode

Abstract: THE various reservoirs of the global carbon cycle, with their very different residence times, are linked by a complex and evolving system of exchanges for which natural radiocarbon is the most robust tracer1. Any change in the sizes of these reservoirs, or the exchange rates between them, could perturb the 14C/12C ratio of each other reservoir, and the smallest of them—the atmosphere— would be the most sensitive. In particular, high-resolution reconstructions of past atmospheric 14C/12C ratios may provide important clues to the mechanisms of abrupt climate change. Annually laminated lake sediments potentially provide an optimal record in this respect, as they preserve information about both past atmospheric 14C levels and climate changes, providing absolutely dated material beyond the range of tree-ring chronologies and, unlike corals, directly monitor 14C concentrations in atmospheric CO2. Here we report the relationship between atmospheric 14C concentration and climate changes during the Younger Dryas and early Holocene periods, derived from analyses of the annually laminated sediments of Lake Gśoscia¸azz, in central Poland. We find that atmospheric 14C concentrations during the Younger Dryas were abnormally high, which we interpret as a reduced ventilation rate of the deep ocean, most probably as a result of a decrease in intensity of the North Atlantic Deep Water formation.

Formal Specification of Multi-Agent Systems: a Real World Case

Abstract: In this paper the framework DESIRE, originally designed for formal specification of complex reasoning systems is used to specify a real-world multi-agent application on a conceptual level. Some extensions to DESIRE are introduced to obtain a useful formal specification framework for multi-agent systems.

Finite supersymmetric threshold corrections to CKM matrix elements in the large tan beta regime.

Abstract: We evaluate the finite one-loop threshold corrections, proportional to tan\ensuremath{\beta}, to the down quark mass matrix. These results in corrections to down quark masses and to Cabibbo-Kobayashi-Maskawa (CKM) matrix elements. The corrections to CKM matrix elements are the novel feature of this paper. For grand unified theories with large tan\ensuremath{\beta} these corrections may significantly alter the low energy predictions of four of the CKM matrix elements and the Jarlskog parameter J, a measure of CP violation. The angles \ensuremath{\alpha}, \ensuremath{\beta}, and \ensuremath{\gamma} of the unitarity triangle and the ratio \ensuremath{\Vert}${\mathit{V}}_{\mathit{u}\mathit{b}}$/${\mathit{V}}_{\mathit{c}\mathit{b}}$\ensuremath{\Vert}, however, are not corrected to this order. We also discuss these corrections in the light of recent models for fermion masses. Here the corrections may be useful in selecting among the various models. Moreover, if one model fits the data, it will only do so for a particular range of SUSY parameters.

The influence of macrophytes on a phytoplankton community in experimental conditions

Abstract: The impact of submerged macrophytes or their extracts on planktonic algae was studied under experimental conditions. Live Ceratophyllum demersum L., its extract, and extracts of four other plant species induced modifications in the phytoplankton dominance structure. These modifications were: a decline in the number of Oscillatoria limnetica Lemm., which was the most numerous cyanobacterian species, and a decline in biomass and percentage contribution of all cyanobacteria to total algal biomass. This was accompanied by an increase in biomass and percentage contribution of green algae, especially Chlorella sp. and Chlamydomonas sp. Also, there was an increase in biomass and percentage contribution of nanoplankton (under 50 µm) to total phytoplankton biomass. The isolation of planktonic algae from direct influence of C. demersum by means of dialysis membranes caused an increase in number, biomass and percentage contribution of cyanobacteria. Release of organic compounds of over 3000 daltons by macrophytes apparently contributed to a decline of cyanobacteria by changing the phytoplankton dominance structure.

Extracting laws from decision tables: a rough set approach

Abstract: We present some methods, based on the rough set and Boolean reasoning approaches, for extracting laws from decision tables. First we discuss several procedures for decision rules synthesis from decision tables. Next we show how to apply some near-to-functional relations between data to data filtration. Two methods of searching for new classifiers (features) are described: searching for new classifiers in a given set of logical formulas, and searching for some functions approximating near-to-functional relations.

C*-algebras generated by unbounded elements

Abstract: The main aim of this paper is to provide a proper mathematical framework for the theory of topological non-compact quantum groups, where we have to deal with non-unital C*-algebras. The basic concepts and results related to the affiliation relation in the C*-algebra theory are recalled. In particular natural topologies on the set of affiliated elements and on the set of morphisms are considered. The notion of a C*-algebra generated by a finite sequence of unbounded elements is introduced and investigated. It is generalized to include continuous quantum families of generators. An essential part of the duality theory for C*-algebras is presented including complete proofs of many theorems announced in [17]. The results are used to develop a presentation method of introducing non-unital C*-algebras. Numerous examples related mainly to the quantum group theory are presented.

The Formal Characteristics of Behaviour—Temperament Inventory (FCB—TI): Validity studies

Abstract: A psychometric study has been conducted with the aim of testing the validity of the Formal Characteristics of Behaviour—Temperament Inventory (FCB—TI). FCB—TI has been constructed to measure six temperament traits according to the Regulative Theory of Temperament (RTT): Briskness, Perseverance (referring to the temporal aspect of behavior), Sensory Sensitivity, Emotional Reactivity, Endurance, and Activity (referring to the energetic characteristics of behaviour). These traits have been compared with other temperament as well as personality dimensions. The following measures were used: PTS, EAS—TS, DOTS—R, EPQ—R, SSS—V, 16PF, and NEO-FFI. The study was conducted on samples consisting of over 1500 subjects with satisfactory balanced gender ratio (about 50 per cent), and with a broad range of age (from 15 to 77 years), representing a variety of professions and educational levels. The correlational and factor analytic findings are presented; these show high theoretical validity of the FCB—TI scales, except the Sensory Sensitivity scale. In the discussion some conclusions concerning the revision of the structure of temperament have been suggested.

Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets

Abstract: Various existing derivations of the effective potentials of mean force for the two-body interactions between amino acid side chains in proteins are reviewed and compared to each other. The differences between different parameter sets can be traced to the reference state used to define the zero of energy. Depending on the reference state, the transfer free energy or other pseudo-one-body contributions can be present to various extents in two-body parameter sets. It is, however, possible to compare various derivations directly by concentrating on the "excess" energy-a term that describes the difference between a real protein and an ideal solution of amino acids. Furthermore, the number of protein structures available for analysis allows one to check the consistency of the derivation and the errors by comparing parameters derived from various subsets of the whole database. It is shown that pair interaction preferences are very consistent throughout the database. Independently derived parameter sets have correlation coefficients on the order of 0.8, with the mean difference between equivalent entries of 0.1 kT. Also, the low-quality (low resolution, little or no refinement) structures show similar regularities. There are, however, large differences between interaction parameters derived on the basis of crystallographic structures and structures obtained by the NMR refinement. The origin of the latter difference is not yet understood.

Time-odd components in the mean field of rotating superdeformed nuclei.

Abstract: Rotation-induced time-odd components in the nuclear mean field are analyzed using the Hartree-Fock cranking approach with effective interactions SIII, SkM*, and SkP. Identical dynamical moments ${\mathcal{J}}^{(2)}$ are obtained for pairs of superdeformed bands $^{151}\mathrm{Tb}$(2)${\mathrm{\ensuremath{-}}}^{152}$Dy(1) and $^{150}\mathrm{Gd}$(2)${\mathrm{\ensuremath{-}}}^{151}$Tb(1). The corresponding relative alignments strongly depend on which time-odd mean-field terms are taken into account in the Hartree-Fock equations.

Squares, cubes, and time-space efficient string searching

Abstract: We address several technical problems related to the time-space optimal string-matching algorithm of Galil and Seiferas (called the GS algorithm). This algorithm contains a parameterk on which the complexity depends and that originally satisfiesk ≥ 4. We show thatk=3 is the least integer for which the GS algorithm works. This value of the parameterk also minimizes the time of the search phase of the string-searching algorithm. With the parameterk=2 we consider a simpler version of the algorithm working in linear time and logarithmic space. This algorithm is based on the following fact: any word of lengthn starts by less than logΦn squares of primitive prefixes. Fibonacci words have a logarithmic number of square prefixes. Hence, the combinatorics of prefix squares and cubes is essential for string-matching with small memory.

Moving Between Logical Systems

Abstract: This paper presents a number of concepts of a mapping between logical systems modelled as institutions, discusses their mutual merits and demerits, and sketches their role in the process of system speciication and development. Some simple properties of the resulting categories of institutions are given.

Transverse energy production in 208Pb+Pb collisions at 158 GeV per nucleon.

Abstract: Author(s): Margetis, S.; Alber, T.; Appelshauser, H.; Bachler, J.; Bartke, J.; Bialkowska, H.; Bieser, F.; Bloomer, M.A.; Blyth, C.O.; Bock, R.; Bormann, C.; Brady, F.P.; Brockmann, R.; Buncic, P.; Caines, H.L.; Cebra, D.; Chan, P.; Cooper, G.E.; Cramer, J.G.; Cramer, P.B.; Csato, P.; Derado, I.; Dunn, J.; Eckardt, V.; Eckhardt, F.; Euler, S.; Ferguson, M.I.; Fischer, H.G.; Fodor, Z.; Foka, P.; Freund, P.; Fuchs, M.; Gal, J.; Gasdzicki, M.; Gladysz, E.; Grebieszkow, J.; Gunther, J.; Harris, J.W.; Heck, W.; Hegyi, S.; Hill, L.A.; Huang, I.; Howe, M.A.; Igo, G.; Irmscher, D.; Jacobs, P.; Jones, P.G.; Kadija, K.; Kecskemeti, J.; Kowalski, M.; Kuhmichel, A.; Lsdiuk, B.; Margetis, S.; Mitchell, J.W.; Mock, A.; Nelson, J.M.; Odyniec, G.J.; Palinkas, J.; Palla, G.; Panagiotou, A.D.; Petridis, A.; Piper, A.; Poskanzer, A.M.; Prindle, D.J.; Puhlhofer, F.; Rauch, W.; Renfordt, R.; Retyk, W.; Ritter, Hans G.; Rohrich, D.; Rudolph, H.; Runge, K.; Sandoval, A.; Sann, H.; Schafer, E.; Schmitz, N.; Schonfelder, S.; Seyboth, P.; Seyerlein, J.; Sikler, F.; Skrzypczak, E.; Stock, R.; Stroebele, H.; Szentpetery, I.; Sziklai, J.