Showing papers by "University of Warsaw published in 2000"

How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules

Abstract: In this study, we present conformational energies for a molecular mechanical model (Parm99) developed for organic and biological molecules using the restrained electrostatic potential (RESP) approach to derive the partial charges. This approach uses the simple "generic" force field model (Parm94), and attempts to add a minimal number of extra Fourier components to the torsional energies, but doing so only when there is a physical justification. The results are quite encouraging, not only for the 34-molecule set that has been studied by both the highest level ab initio model (GVB/LMP2) and experiment, but also for the 55-molecule set for which high-quality experimental data are available. Considering the 55 molecules studied by all the force field models for which there are experimental data, the average absolute errors (AAEs) are 0.28 (this model), 0.52 (MM3), 0.57 (CHARMm (MSI)), and 0.43 kcal/mol (MMFF). For the 34-molecule set, the AAEs of this model versus experiment and ab initio are 0.28 and 0.27 kcal/mol, respectively. This is a lower error than found with MM3 and CHARMm, and is comparable to that found with MMFF (0.31 and 0.22 kcal/mol). We also present two examples of how well the torsional parameters are transferred from the training set to the test set. The absolute errors of molecules in the test set are only slightly larger than in the training set (differences of <0.1 kcal/mol). Therefore, it can be concluded that a simple "generic" force field with a limited number of specific torsional parameters can describe intra- and intermolecular interactions, although all comparison molecules were selected from our 82-compound training set. We also show how this effective two-body

Dynamic Logic

Abstract: From the Publisher: Among the many approaches to formal reasoning about programs, Dynamic Logic enjoys the singular advantage of being strongly related to classical logic. Its variants constitute natural generalizations and extensions of classical formalisms. For example, Propositional Dynamic Logic (PDL) can be described as a blend of three complementary classical ingredients: propositional calculus, modal logic, and the algebra of regular events. In First-Order Dynamic Logic (DL), the propositional calculus is replaced by classical first-order predicate calculus. Dynamic Logic is a system of remarkable unity that is theoretically rich as well as of practical value. It can be used for formalizing correctness specifications and proving rigorously that those specifications are met by a particular program. Other uses include determining the equivalence of programs, comparing the expressive power of various programming constructs, and synthesizing programs from specifications. This book provides the first comprehensive introduction to Dynamic Logic. It is divided into three parts. The first part reviews the appropriate fundamental concepts of logic and computability theory and can stand alone as an introduction to these topics. The second part discusses PDL and its variants, and the third part discusses DL and its variants. Examples are provided throughout, and exercises and a short historical section are included at the end of each chapter.

Template-based synthesis of nanomaterials

Abstract: The large interest in nanostructures results from their numerous potential applications in various areas such as materials and biomedical sciences, electronics, optics, magnetism, energy storage, and electrochemistry. Ultrasmall building blocks have been found to exhibit a broad range of enhanced mechanical, optical, magnetic, and electronic properties compared to coarser-grained matter of the same chemical composition. In this paper various template techniques suitable for nanotechnology applications with emphasis on characterization of created arrays of tailored nanomaterials have been reviewed. These methods involve the fabrication of the desired material within the pores or channels of a nanoporous template. Track-etch membranes, porous alumina, and other nanoporous structures have been characterized as templates. They have been used to prepare nanometer-sized fibrils, rods, and tubules of conductive polymers, metals, semiconductors, carbons, and other solid matter. Electrochemical and electroless depositions, chemical polymerization, sol-gel deposition, and chemical vapour deposition have been presented as major template synthetic strategies. In particular, the template-based synthesis of carbon nanotubes has been demonstrated as this is the most promising class of new carbon-based materials for electronic and optic nanodevices as well as reinforcement nanocomposites.

Tau neutrinos favored over sterile neutrinos in atmospheric muon neutrino oscillations.

Abstract: The previously published atmospheric neutrino data did not distinguish whether muon neutrinos were oscillating into tau neutrinos or sterile neutrinos, as both hypotheses fit the data. Using data recorded in 1100 live days of the Super-Kamiokande detector, we use three complementary data samples to study the difference in zenith angle distribution due to neutral currents and matter effects. We find no evidence favoring sterile neutrinos, and reject the hypothesis at the $99%$ confidence level. On the other hand, we find that oscillation between muon and tau neutrinos suffices to explain all the results in hand.

Rough set algorithms in classification problem

Abstract: We we present some algorithms, based on rough set theory, that can be used for the problem of new cases classification. Most of the algorithms were implemented and included in Rosetta system [43]. We present several methods for computation of decision rules based on reducts. We discuss the problem of real value attribute discretization for increasing the performance of algorithms and quality of decision rules. Finally we deal with a problem of resolving conflicts between decision rules classifying a new case to different categories (classes). Keywords: knowledge discovery, rough sets, classification algorithms, reducts, decision rules, real value attribute discretization

Evidence for melatonin synthesis in mouse and human bone marrow cells.

Abstract: Recently, it was demonstrated that inbred strains of mice have a clearcut circadian rhythm of pineal and serum melatonin. Moreover, it is known that melatonin is involved in many immunoregulatory functions. Among them, hematopoiesis is influenced by the action of melatonin via melatonin-induced opioids on kappa-opioid receptors, which are present on stromal bone marrow cells. Therefore, the present study was carried out to investigate the presence of melatonin in the bone marrow in which immunocompetent cells are generated. Specifically, we aimed at answering the following question: are bone marrow cells involved in melatonin synthesis? In the present study, we demonstrate that (1) bone marrow cells contain high concentrations of melatonin; (2) bone marrow cells have a N-acetyltransferase activity and they express the mRNA encoding hydroxy-O-methyltransferase and (3) bone marrow cells cultured for a prolonged period exhibited high levels of melatonin. Results presented here suggest that mouse and human bone marrow and bone marrow cells are capable of de novo synthesis of melatonin, which may have intracellular and or paracrine functions.

Gauge Field Theories

Abstract: Preface Introduction 1. Classical fields, symmetries and their breaking 2. Path integral formulation of quantum field theory 3. Feynman rules for Yang-Mills theories 4. Introduction to the theory of renormalization 5. Quantum electrodynamics 6. Renormalization group 7. Scale invariance and operator product expansion 8. Quantum chromodynamics 9. Chiral symmetry, spontaneous symmetry breaking 10. Spontaneous and explicit global symmetry breaking 11. Higgs mechanisms in gauge theories 12. Standard electroweak theory 13. Chiral anomalies 14. Effective lagrangians 15. Introduction to supersymmetry Appendices.

Generic isolated horizons and their applications

Abstract: The notion of isolated horizons is extended to allow for distortion and rotation. Space-times containing a black hole, itself in equilibrium but possibly surrounded by radiation, satisfy these conditions. The framework has three types of applications: (i) it provides new tools to extract physics from strong field geometry; (ii) it leads to a generalization of the zeroth and first laws of black hole mechanics and sheds new light on the “origin” of the first law; and (iii) it serves as a point of departure for black hole entropy calculations in nonperturbative quantum gravity.

Structural Genomics and Its Importance for Gene Function Analysis

Abstract: Structural genomics projects aim to solve the experimental structures of all possible protein folds. Such projects entail a conceptual shift from traditional structural biology in which structural information is obtained on known proteins to one in which the structure of a protein is determined first and the function assigned only later. Whereas the goal of converting protein structure into function can be accomplished by traditional sequence motif-based approaches, recent studies have shown that assignment of a protein's biochemical function can also be achieved by scanning its structure for a match to the geometry and chemical identity of a known active site. Importantly, this approach can use low-resolution structures provided by contemporary structure prediction methods. When applied to genomes, structural information (either experimental or predicted) is likely to play an important role in high-throughput function assignment.

Exponential and Moment Inequalities for U-Statistics

Abstract: A Bernstein-type exponential inequality for (generalized) canonical U-statistics of order 2 is obtained, and the Rosenthal and Hoffmann-Jorgensen inequalities for sums of independent random variables are extended to (generalized) U-statistics of any order whose kernels are either nonnegative or canonical.

Structure of binary Bose-Einstein condensates

Abstract: We identify all possible classes of solutions for two-component Bose-Einstein condensates (BECs) within the Thomas-Fermi (TF) approximation and check these results against numerical simulations of the coupled Gross-Pitaevskii equations (GPEs). We find that they can be divided into two general categories. The first class contains solutions with a region of overlap between the components. The other class consists of non-overlapping wavefunctions and also contains solutions that do not possess the symmetry of the trap. The chemical potential and average energy can be found for both classes within the TF approximation by solving a set of coupled algebraic equations representing the normalization conditions for each component. A ground state minimizing the energy (within both classes of states) is found for a given set of parameters characterizing the scattering length and confining potential. In the TF approximation, the ground state always shares the symmetry of the trap. However, a full numerical solution of the coupled GPEs, incorporating the kinetic energy of the BEC atoms, can sometimes select a broken-symmetry state as the ground state of the system. We also investigate effects of finite-range interactions on the structure of the ground state.

Shell corrections of superheavy nuclei in self-consistent calculations

Abstract: Shell corrections to the nuclear binding energy as a measure of shell effects in superheavy nuclei are studied within the self-consistent Skyrme-Hartree-Fock and relativistic mean-field theories. As a result of the presence of a low-lying proton continuum resulting in a free particle gas, special attention is paid to the treatment of the single-particle level density. To cure the pathological behavior of the shell correction around the particle threshold, a method based on the Green's function approach has been adopted. It is demonstrated that for the vast majority of Skyrme interactions commonly employed in nuclear structure calculations, the strongest shell stabilization appears for Z=124 and 126, and for N=184. On the other hand, in the relativistic approaches the strongest spherical shell effect appears systematically for Z=120 and N=172. This difference probably has its roots in the spin-orbit potential. We have also shown that, in contrast to shell corrections which are fairly independent of the force, macroscopic energies extracted from self-consistent calculations strongly depend on the actual force parametrization used. That is, the A and Z dependence of the mass surface when extrapolating to unknown superheavy nuclei is prone to significant theoretical uncertainties. (c) 2000 The American Physical Society.

Between Sobolev and Poincaré

Abstract: Let a a ∈ [0, 1] and r ∈ [1, 2] satisfy relation r = 2/(2 − a). Let μ(dx)=c r n exp(-(|x1| r +|x2| r +...+|x n | r ))dx1dx2...dx n be a probability measure on the Euclidean space (R n , ‖ · ‖). We prove that there exists a universal constant C such that for any smooth real function f on R n and any p ∈ [1,2) $$E_\mu f^2 - (E_\mu \left| f \right|^p )^{2/p} \leqslant C(2 - p)^a E_\mu \left\| { abla f} \right\|^2$$ . We prove also that if for some probabilistic measure μ on R n the above inequality is satisfied for any p ∈ [1, 2) and any smooth f then for any h : R n → R such that |h(x)-h(y)|≤∥x-y∥ there is E μ |h| < ∞ and $$\mu (h - E_\mu h > \sqrt C \cdot t) \leqslant e^{ - Kt^r }$$ for t > 1, where K > 0 is some universal constant.

RSES and RSESlib - A Collection of Tools for Rough Set Computations

Abstract: Rough Set Exploration System - a set of software tools featuring a library of methods and a graphical user interface is presented. Methods, features and abilities of the implemented software are discussed and illustrated with a case study in data analysis.

Reconstructing the chargino system at $e^+e^-$ linear colliders

Abstract: In most supersymmetric theories charginos, \(\tilde{\chi}^\pm_{1,2}\), belong to the class of the lightest supersymmetric particles. The chargino system can be reconstructed completely in \(e^+e^-\) collider experiments: \(e^+e^-\rightarrow\tilde{\chi}_i^+ \tilde{\chi}_j^- \, \, [i,j=1,2]\). By measuring the total cross sections and the asymmetries with polarized beams, the chargino masses and the gaugino–higgsino mixing angles of these states can be determined accurately. If only the lightest charginos \(\tilde{\chi}_1^\pm\) are kinematically accessible in a first phase of the machine, transverse beam polarization or the measurement of chargino polarization in the final state is needed to determine the mixing angles. From these observables the fundamental SUSY parameters can be derived: the SU(2) gaugino mass \(M_2\), the modulus and the cosine of the CP–violating phase of the higgsino mass parameter \(\mu\), and \(\tan\beta = v_2/v_1\), the ratio of the vacuum expectation values of the two neutral Higgs doublet fields. The remaining two–fold ambiguity of the phase can be resolved by measuring the normal polarization of the charginos. Sum rules of the cross sections can be exploited to investigate the closure of the two–chargino system.