Improving the Round Trip Time Estimation in Internet Routers

Author: Darius Bufnea / Adrian Sterca / Claudiu COBÂRZAN / FLORIAN BOIAN

Abstract: We review in this paper the concept of TCP-friendliness and we debate one of
its weaknesses. Unfortunately, this weakness reduces the practical applicability of the TCP-
friendliness equation. For a very high percent of the Internet flows, the TCP-friendliness test may
have wrong results. We suggest in this paper a router algorithm that improves the efficiency of the
TCP-friendliness equation for some UDP flows. This algorithm uses the additional information
retrieved by the router from competing TCP flows in order to obtain a better approximation for
the round trip time as used in the TCP-friendliness test. PDF |

Link-Cell Method for Evolutionary Multi-Modal Optimization Application in Dynamic Evolutionary Clustering

Author: Dan Dumitrescu / Ferenc Jarai-Szabo / Karoly Simon

Abstract: Evolutionary algorithms can be successfully used for solving multi-modal opti-
mization problems. Inspired from Computational Physics a Link-Cell-based method is proposed
in order to obtain improved evolutionary multi-modal optimization models. Recently a new evo-
lutionary search and multi-modal optimization metaheuristics - called Genetic Chromodynamics
(GC) - has been proposed and used to derive new evolutionary algorithms. Based on the GC
metaheuristics a new dynamic evolutionary clustering technique has been developed. The pro-
posed Link-Cell technique is combined with GC. In this way a new evolutionary multi-modal
optimization model is obtained. This model is applied to GC-based dynamic clustering method
(GCDC) and a new Link-Cell-based GCDC algorithm is developed. Some numerical experiments
are described. PDF |

About the Dirichlet and Neumann boundary value problems expressed by means of monogenous quaternions

Author: Lidia Elena Kozma

Abstract: Using the solution of Dirichlet’s plane problem, the solution given as a monogenous
surface, we obtain the solution of Neumann’s plane problem through the rotation of the quater-
nion associated to the solution of Dirichlet’s problem. PDF |

Abstract: Specifying a real-world component system is a complex manual process. It is
essential to be able to verify the correctness and robustness of its behavior, before it becomes
operational. We propose a new way of specifying a component system, based on the concept
of interface, that can be seen as a tool from analysis and design to programming and for type
specification. We construct an algorithm that constructs the model, and can be used to deduct
properties about the system: correctness, termination, deadlock free. PDF |

On a matrix representation of molecular structures

Author: Zoița Berinde / Mădălina Berinde

Abstract: In order to discriminate molecular structures containing multiple bonds and het-
eroatoms, the paper considers the weighted electronic connectivity matrix (CEP). This matrix
is obtained by replacing the classical topological distance by the so called weighted electronic
distance (w.e.d). The CEP matrix can be then used for obtaining several topological indices
[10]. PDF |

Author: Marcela F. Dinca / Simona Ciger / Monica Stefu / F. Gherman / Katalin Miklos / Csaba L. N

Abstract: The well-known “isolated pentagon rule” IPR is described in quantitative terms
provided by the layer matrix of valences, constructed on the dual of the associate molecular graph of
fullerenes. The derived pentagon valence pv parameter correlates well (it describes more than 90%
of variance) with the PM3 heat of formation of small fullerenes C40. The equivalence classes of their
vertices, edges and faces are also deducible from some layer matrix invariants. They are important
in simulating the 13C NMR spectrum and/or in predicting the products of addition reactions of
fullerenes.1 PDF |

Author: Mircea V. Diudea / Duanska Janeie / Ante Graovac

Abstract: Tubulenes are capped nanotubes built up from two caps and a distancing
nanotube/neck of diverse decoration. Ways of “in silico” construction of several finite
nanostructures, classified by their neck and/or caps, are presented. Topological periodicity is
presented as constitutive typing enumeration. Semiempirical calculations support the idea that new,
relatively stable molecules may appear in the soot of vaporized graphite. PDF |

The Second Path Matrix of the Graph and its Characteristic Polynomial

Author: Peter E. John / Mircea V. Diudea

Abstract: The second path matrix S(G) collects all the second paths in the graph G. Its
characteristic polynomial shows some regularity in several particular graphs, such as paths, cycles,
stars and complete graphs, as well as in bipartite graphs. Formulas for calculating the characteristic
polynomials in these graphs are given. The first eigenvalue of S(G) showed an excellent correlating
ability. PDF |

Theoretical Study on Phosphorus Substitutionally Doped Fullerenes

Author: Liliana Pacureanu / Mircea V. Diudea / Mircea Mracec

Abstract: Since Karfunkel predicted the stability of azafullerenes by semiempirical calculation, a
sustaining effort was paid to quantum-chemical calculation of substitutionally dopped fullerenes.
While the N and B hetero-fullerenes are the most known, in the last years Si, Co, Ni, Fe, Rh, Ir
dopped C60 have been modeled.4-6
This paper reports semiempirical PM3 calculations of phosphorus substituted fullerenes C60-
nPn, n = 1-6. The C by P replacement appears to not dramatically influence the thermal stability of
substituted C60 but electronic structure is changed. The degeneracy of HOMO and LUMO levels is
reduced or destroyed while the HOMO-LUMO gap is, in some cases, as high as in the parent C60
and consistent with a good kinetic stability. The difference between C and P electronegativity
determines the partial positive charge at phosphorus and a negative charge at the neighboring C
atoms. The displacement of a number of phosphorus atoms on the same polygon diminishes the
positive charge at phosphorus. Angles at phosphorus are larger when phosphorus is on a hexagon.
The reverse situation is found for bond length that increases for P-C [5,6] with respect to [6,6]
bonds. The bonding energy of P-dopped fullerenes decrease with increasing the number of
phosphorus atoms, as the strength of P-C bonds decreases with respect to C-C bonds. From
energetic considerations, we can draw the conclusion that phosphorus dopped fullerenes may be
stable molecules. PDF |

Abstract: The encapsulation of fullerene cages inside single-walled nanotubes SWNT can be
performed very efficiently in both vapor phase and in solution. In the inner space of SWNT, zero
dimensional molecules, like C60, are ordered in one-dimensional arrays. Such structures are called
nanopeapods. Annealing peapods over 800oC, results in double-walled carbon nanotubes DWNT.
We propose that controlled irradiation at the tip of nano-peapods could initiate the fusion between
the inner and parent nanotube, resulting a torus.1 PDF |

Abstract: We present a new detection method of amino acid residues, which play the role of the
protein functional activities. The principle of the method is that proteins with the same function
have similar amino acid residues at the similar 3D positions. Thus we assume that maximal amino
acid residues existing in the similar 3D positions of proteins are their function site residues. The
method first constructs the graph describing relations of 3D positions of all possible pairs of amino
acid residues in two proteins and then extracts its maximal complete subgraph, which means the
maximal amino acid residues at the similar three dimensional positions, by the algorithm of
Carraghan and Pardalos.
The method was tested using electron transport proteins: azurin and plastocyanin, and 6
reasonable amino acid residues as the function site residues of those proteins, were obtained. The
method was also applied to acid proteases: porcine pepsin and Rhizopus pepsin. In this
investigation, we restricted the formation of amino acid pairs only to the same ones, because of the
limitation of computer memory. The result gave 11 amino acid residues, consisting in some active
site residues, as the function residues of acid proteases. The results indicate the effectiveness of this
new method. PDF |

QSARs of some Novel Isosteric Heterocyclic with Antifungal Activity

Author: Oleg Ursu / Adina Costescu / Mircea V. Diudea / Bazil Parv

Abstract: QSAR analysis of a set of 2,5,6-trisubstituted benzoxazoles, benzimidazoles and 2-
substituted oxazolo(4,5-b)pyridines, tested for growth inhibitory activity against Candida albicans,
was performed by using a multiple regression procedure. The activity contributions for either
heterocyclic ring systems or substituent effects of these compounds were determined from the
correlation equations and the lead optimization is described. The obtained QSAR revealed that the
oxazolo(4,5-b)pyridine ring, substituted by a benzyl moiety at position 2, was the most favorable
structure among the heterocyclic nuclei. Moreover, the fifth position in the fused ring system is
found more significant than the other positions in rising up the activity. PDF |

Author: Oleg Ursu / Marinela Don / Gabriel Katona / Lorentz Jantschi / Mircea V. Diudea

Abstract: Quantitative Structure-Activity Relationships (QSARs) establish a mathematical relation
between the biological activity of chemical compounds and their molecular structure. They provide
quantitative models aimed to accurately predict a certain activity from the structural attributes. This
topic has become a well-delimited branch in chemistry and was favored by the progress in computer
science. Cluj property indices are used for modeling the ACE inhibition biological activity of a set
of 58 dipeptides, taken from the literature. Description of dipeptide molecules is made by using the
fragmental property Cluj indices. Four models were taken into consideration: two of them
topological (dense topological and rare topological) and two others geometric (dense geometric and
rare geometric). In these models, a weak dependence on distance for the potential function
(gravitational and Coulombian), in uniform field, and a strong dependence on distance for the
potential, that generates a non-uniform field, were considered. The indices are calculated as local
descriptors of some fragments of the molecule and, a global index is then obtained by summing the
fragmental contributions. The statistics were performed by STATISTICA software package. The
results are compared to those reported in some previous works. PDF |

Quantitative Structure-Activity Relationship Study of COX-2 Inhibitors

Author: Oleg Ursu / Mircea V. Diudea / Shin-Ichi Nakayma

Abstract: Quantitative Structure-Activity Relationship (QSAR) is a tool used with success to model
biological activity of series of compounds. There is a serious limitation in the use of this method – it
works well only on series of highly homogenous compounds. To furnish such sets of structures,
several similarity classification schemes have been proposed: Naïve Bayesian classifier, artificial
neural networks, molecular fingerprints, and maximum overlapping structures method, MOS. The
most accurate classifier MOS is the most computationally demanding as well, and until recently its
use was limited. Recent development of the algorithm introduced a series of heuristics and a new
rapid clique detection procedure led to significant improvements in the speed of MOS, thus making
it suitable for virtual screening of large databases of molecules. In the present study we make use of
the MOS method to classify unknowns according to their structural features into classes of
structurally homogeneous compounds suitable for further analysis by classical QSAR approaches. PDF |

Evaluation of the DWT filters
for image compression

Author: Ovidiu Cosma

Abstract: The characteristics of the digital filter used for computing the Discrete Wavelet Transform (DWT) determine the performance of the compression scheme. This article presents an evaluation of the DWT filters, from an image compression point of view.