Local Hybrid Divide-and-Conquer Method for the Computation of Medium and Large Molecules

2008 ◽  
Vol 4 (12) ◽  
pp. 2049-2056 ◽  
Author(s):  
Guo-Liang Song ◽  
Zhen Hua Li ◽  
Zhi-Pan Liu ◽  
Xiao-Ming Cao ◽  
Wenning Wang ◽  
...  
Keyword(s):  
Divide And Conquer ◽  
Large Molecules

LINEAR SCALING FOR DENSITY FUNCTIONAL CALCULATIONS ON LARGE MOLECULES WITH THE DEFT SOFTWARE PACKAGE

2004 ◽  
Vol 03 (03) ◽  
pp. 419-442 ◽  
Author(s):  
DAWN M. SHAW ◽  
ALAIN ST-AMANT
Keyword(s):  
Software Package ◽  
Density Functional ◽  
System Size ◽  
Divide And Conquer ◽  
Basis Sets ◽  
Linear Scaling ◽  
Large Molecules ◽  
Density Fitting ◽  
Inherent Error ◽  
Functional Software

The new methods implemented within the DeFT density functional software package are outlined. Where appropriate, they are benchmarked against the conventional methods, which are prohibitively expensive for large systems due to their poor scaling with system size. Benchmark calculations on extended glycine polypeptides clearly demonstrate that linear scaling has been achieved for these first principles electronic structure calculations. Within the DeFT software package, a divide-and-conquer approach is instrumental in attaining this goal. The errors introduced by our divide-and-conquer approach are quantified and shown to be insignificant when compared to the inherent error in even the most accurate density functionals presently available. Calculations on molecules within the G2 dataset highlight the overall accuracy of the exchange-correlation functionals, orbital basis sets, auxiliary density fitting basis sets, and grids used within DeFT.

The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

HES 200/0.5 Is not HES 200/0.5

1995 ◽  
Vol 74 (06) ◽  
pp. 1452-1456 ◽  
Author(s):  
Johannes Treib ◽  
Anton Haass ◽  
Gerhard Pindur ◽  
Ulrich T Seyfert ◽  
Wolfgang Treib ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Hydroxyethyl Starch ◽  
Clinical Relevance ◽  
Dilution Effect ◽  
Repeated Administration ◽  
Plasma Viscosity ◽  
Degree Of Substitution ◽  
Pronounced Increase ◽  
Large Molecules ◽  
Mean Molecular Weight

SummaryThe plasma clearance of hydroxyethyl starch (HES) depends on the initial molecular weight and the degree of substitution. So far, little attention has been paid to the clinical relevance of the C2/C6 substitution ratio of hydroxyethyl starch.10 patients with cerebrovascular circulatory disturbance received hemodilution therapy for 10 days, consisting of 10% HES 200/0.5 (mean molecular weight 200 kD, degree of substitution 0.5) with a C2/C6 ratio of 13.4. A second group of 10 patients received a starch solution with identical initial molecular weight and degree of substitution but with a C2/C6 ratio of 5.7.After the administration of a single dose, no significant differences between the two groups were observed. After repeated administration, significant differences could be detected in hemorheology, coagulation and elimination (p<0.01). The larger C2/C6 ratio led to a higher intravascular mean molecular weight (95 vs. 84 kD), which in turn led to a higher increase in serum concentration during the therapy (14.7 vs.8.6 mg/ml). Hematocrit was lowered more (-30,5 vs. -23,5%) and plasma viscosity was increased more. There was also a more pronounced increase in partial thromboplastin time (+30% vs. +13%) and a factor of 2 larger decrease of factor VIII/von Willebrand factor-complex (p <0.01), which exceeded the dilution effect.The higher C2/C6 ratio of HES 200/0.5/13.4 slows down enzymatic degradation. After repeated administration of this starch, large molecules accumulate which are inefficiently degraded. The same effect has been observed after therapy with highly-substituted HES. This accumulation of large molecules leads to a beneficial longer lasting volume effect. The disadvantages include an increase in plasma viscosity and coagulation disturbances, which cannot be explained with the respective dilution effect alone. For these reasons, the C2/C6 ratio is of clinical relevance and should be included in the product labeling in the future.

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