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Consistent Treatment (consistent + treatment)
Selected AbstractsAutomated Alignment and Nomenclature for Consistent Treatment of Polymorphisms in the Human Mitochondrial DNA Control RegionJOURNAL OF FORENSIC SCIENCES, Issue 5 2010Bruce Budowle Ph.D. Abstract:, Naming mtDNA sequences by listing only those sites that differ from a reference sequence is the standard practice for describing the observed variations. Consistency in nomenclature is desirable so that all sequences in a database that are concordant with an evidentiary sequence will be found for estimating the rarity of that profile. The operational alignment and nomenclature rules, i.e., "Wilson Rules," suggested for this purpose do not always guarantee a single consistent sequence description for all observed polymorphisms. In this work, the operational alignment/nomenclature rules were reconfigured to better reflect traditional user preferences. The rules for selecting alignments are described. In addition, to avoid human error and to more efficiently name mtDNA sequence variants, a computer-facilitated method of aligning mtDNA sample sequences with a reference sequence was developed. There were 33 differences between these hierarchical rules and the data in SWGDAM, which translates into a 99.92% consistency between the new rules and the manual historical nomenclature approach. The data support the reliability of the current SWGDAM database. As the few discrepancies were changed in favor of the new hierarchical rules, the quality of the SWGDAM database is further improved. [source] Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2002Pengyu Ren Abstract A protocol is described for the treatment of molecular polarization in force field calculations. The resulting model is consistent in that both inter- and intramolecular polarization are handled within a single scheme. An analytical formula for removing intramolecular polarization from a set of atomic multipoles for an arbitrary static structure or conformation is given. With the help of the intramolecular polarization, these permanent atomic multipoles can then be applied in modeling alternative conformations of a molecule. Equipped with this simple technique, one can derive transferable electrostatic parameters for peptides and proteins using flexible model compounds such as dipeptides. The proposed procedure is tested for its ability to describe the electrostatic potential around various configurations of the N -methylacetamide dimer. The effect of different intramolecular polarization schemes on the accuracy of a force field model of the electrostatic potential of alanine dipeptide is investigated. A group-based scheme for including direct intramolecular polarization is shown to be most successful in accounting for the conformational dependence of electrostatic potentials. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1497,1506, 2002 [source] Statistical theory of weak field thermoremanent magnetization in multidomain particle ensemblesGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 2 2003Karl Fabian SUMMARY A non-equilibrium statistical theory of multidomain thermoremanent magnetization (TRM) is developed, which describes thermal magnetization changes as continuous inhomogeneous Markov processes. The proposed theory relies on three very general physical properties of TRM: (a) The probability that a magnetization state Sj is transformed during an infinitesimal temperature change into state Si depends only on external conditions and on Sj, but not on previously assumed states. (b) Due to time inversion symmetry of the Maxwell equations, the magnetic energies are invariant with respect to inversion of all spins in zero field. (c) The probability that an energy barrier between two magnetization states is overcome during a thermal process is governed by Boltzmann statistics. From these properties, the linearity of TRM with field is derived for generic multidomain particle ensembles. The general validity of Thellier's law of additivity of partial TRM's in weak fields is established and a method for proving a large class of similar additivity laws is developed. The theory allows consistent treatment of blocking and unblocking of remanence in multidomain particle ensembles and naturally explains apparent differences between blocking and unblocking temperatures. [source] A variationally consistent framework for the design of integrator and updates of generalized single step representations for structural dynamicsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 8 2003R. Kanapady Abstract A variationally consistent framework leading to the concise design of both the ,integrator' and the associated ,updates' as related to the single step representations encompassing the so-called LMS methods for structural dynamics is described. The present paper shows for the first time, a consistent treatment involving both the ,integrator' and ,updates' that are inherent in the general context of designing the time integration process. Furthermore, the framework encompasses not only all the existing time integration algorithms that are dissipative and non-dissipative within the scope of LMS methods but also contains new optimal algorithms useful for practical applications,in the sense of accuracy, stability, numerical dissipation and dispersion, and overshoot characteristics of computational algorithms for time dependent problems encountered in structural dynamics. Copyright © 2003 John Wiley & Sons, Ltd. [source] Temperature effects on the UV,Vis electronic spectrum of trans-stilbeneINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001S. P. Kwasniewski Abstract The ultraviolet (UV),Visible absorption spectrum of trans-stilbene (tS) is computed at different temperatures by coupling molecular dynamics (MD) simulations with the classical MM3 force field to ZINDO/S-CIS calculations of vertical excitation energies and transition dipole moments. The selection of a large number of structures along the MD trajectories enables a consistent treatment of temperature effects in the vacuum, whereas the ZINDO/S-CIS calculations permit a reliable treatment of electron correlation and relaxation, taking account of multistate interactions in the final state. Thermal motions are found to alter very differently the width and shape of bands. Structural alterations such as the stretching and the torsion of the vinyl single and double bonds very strongly influence the appearance of the first valence state, pertaining to the highest occupied and lowest unoccupied molecular orbital (HOMO,LUMO) transition. At temperatures less than 400 K, these are found to yield a merely Gaussian and very pronounced thermal broadening of the related band (A), up to nearly 30 nm, together with a minor blue shift of its maximum ,max. In contrast, a red shift by several nanometers occurs due to thermal motions for the remaining three valence bands. As can be expected, the broadening intensifies at higher temperatures, and for the A-band, becomes markedly asymmetric when T exceeds 400 K. The combination of MD(MM3) and ZINDO/S-CIS computations enables also consistent calculations of hot bands, which are forbidden by symmetry at 0 K. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] | ||||||||||