scholarly journals Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors

2006 ◽  
Vol 63 (4) ◽  
pp. 949-960 ◽  
Author(s):  
Jinfeng Zhang ◽  
Rong Chen ◽  
Jie Liang
Keyword(s):  
Potential Function ◽  
Sequence Structure ◽  
Empirical Potential ◽  
Local Sequence ◽  
Protein Models

ADSORPTION AND DIFFUSION OF Si ON THE Si(001): AN EMPIRICAL POTENTIAL CALCULATION

2002 ◽  
Vol 16 (04) ◽  
pp. 621-629 ◽  
Author(s):  
JUN CAI ◽  
JIAN-SHENG WANG
Keyword(s):  
Potential Function ◽  
Binding Sites ◽  
Surface Adsorption ◽  
First Principle ◽  
Empirical Potential ◽  
First Principle Calculations ◽  
Diffusion Paths ◽  
And Diffusion ◽  
Formation Energies ◽  
Diffusion Activation

A recently developed potential function for covalent materials (Phys. Stat. Sol.B212, 9 (1999)) is used to simulate the surface adsorption, and diffusion of Si adtom and ad-dimer on the Si(001) surface. We calculate the formation energies and diffusion activation energies of several possible binding sites. The predicted stable and metastable configurations and diffusion paths of Si ad-atom and Si ad-dimer on Si(001)-(2×1) surface are in agreement with that from the first principle calculations or experiments.

LOCAL SEQUENCE-STRUCTURE MOTIFS IN RNA

2004 ◽  
Vol 02 (04) ◽  
pp. 681-698 ◽  
Author(s):  
ROLF BACKOFEN ◽  
SEBASTIAN WILL
Keyword(s):  
Information Structure ◽  
Structure Alignment ◽  
General Definition ◽  
Local Alignment ◽  
Sequence Information ◽  
Sequence Structure ◽  
Worst Case ◽  
Rna Molecules ◽  
Alignment Algorithms ◽  
Local Sequence

Ribonuclic acid (RNA) enjoys increasing interest in molecular biology; despite this interest fundamental algorithms are lacking, e.g. for identifying local motifs. As proteins, RNA molecules have a distinctive structure. Therefore, in addition to sequence information, structure plays an important part in assessing the similarity of RNAs. Furthermore, common sequence-structure features in two or several RNA molecules are often only spatially local, where possibly large parts of the molecules are dissimilar. Consequently, we address the problem of comparing RNA molecules by computing an optimal local alignment with respect to sequence and structure information. While local alignment is superior to global alignment for identifying local similarities, no general local sequence-structure alignment algorithms are currently known. We suggest a new general definition of locality for sequence-structure alignments that is biologically motivated and efficiently tractable. To show the former, we discuss locality of RNA and prove that the defined locality means connectivity by atomic and non-atomic bonds. To show the latter, we present an efficient algorithm for the newly defined pairwise local sequence-structure alignment (lssa) problem for RNA. For molecules of lengthes n and m, the algorithm has worst-case time complexity of O(n2·m2· max (n,m)) and a space complexity of only O(n·m). An implementation of our algorithm is available at . Its runtime is competitive with global sequence-structure alignment.

scholarly journals An Optimization Synchronization Algorithm for TDDM Signal

2016 ◽  
Vol 2016 ◽  
pp. 1-7
Author(s):  
Fang Liu ◽  
Yongxin Feng
Keyword(s):  
Spread Spectrum ◽  
Sequence Structure ◽  
Estimation Formula ◽  
Synchronization Algorithm ◽  
Local Sequence ◽  
Threshold Mechanism ◽  
Global Navigation Satellite ◽  
Time Division ◽  
Synchronization Accuracy ◽  
Better Than

The time division data modulation (TDDM) mechanism is recommended to improve the communications quality and enhance the antijamming capability of the spread spectrum communication system, which will be used in the next generation global navigation satellite (GNSS) systems. According to the principle and the characteristics of TDDM signal, an optimization synchronization algorithm is proposed. In the new algorithm, the synchronization accuracy and environmental adaptability have been improved with the special local sequence structure, the multicorrelation processing, and the proportion threshold mechanism. Thus, the inversion estimation formula was established. The simulation results demonstrate that the new algorithm can eliminate the illegibility threat in the synchronization process and can adapt to a lower SNR. In addition, this algorithm is better than the traditional algorithms in terms of synchronization accuracy and adaptability.

Forces in Molecules. III. Analysis of an Empirical Potential Function

1963 ◽  
Vol 39 (12) ◽  
pp. 3316-3321 ◽  
Author(s):  
William L. Clinton ◽  
Sandra D. Frattali
Keyword(s):  
Potential Function ◽  
Empirical Potential
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