scholarly journals SCEDS: protein fragments for molecular replacement inPhaser

2013 ◽  
Vol 69 (11) ◽  
pp. 2216-2225 ◽  
Author(s):  
Airlie J. McCoy ◽  
Robert A. Nicholls ◽  
Thomas R. Schneider
Keyword(s):  
Normal Modes ◽  
Low Frequency ◽  
Distance Matrix ◽  
Triaxial Ellipsoid ◽  
Molecular Replacement ◽  
Elastic Network Model ◽  
Protein Fragments ◽  
Template Model ◽  
Invariant Regions ◽  
The Difference

A method is described for generating protein fragments suitable for use as molecular-replacement (MR) template models. The template model for a protein suspected to undergo a conformational change is perturbed along combinations of low-frequency normal modes of the elastic network model. The unperturbed structure is then compared with each perturbed structure in turn and the structurally invariant regions are identified by analysing the difference distance matrix. These fragments are scored with SCEDS, which is a combined measure of the sphericity of the fragments, the continuity of the fragments with respect to the polypeptide chain, the equality in number of atoms in the fragments and the density of Cαatoms in the triaxial ellipsoid of the fragment extents. The fragment divisions with the highest SCEDS are then used as separate template models for MR. Test cases show that where the protein contains fragments that undergo a change in juxtaposition between template model and target, SCEDS can identify fragments that lead to a lowerRfactor after ten cycles of all-atom refinement withREFMAC5 than the original template structure. The method has been implemented in the softwarePhaser.

scholarly journals Analysis of Low-Frequency Mutations Associated with Drug Resistance to Raltegravir before Antiretroviral Treatment

2010 ◽  
Vol 55 (3) ◽  
pp. 1114-1119 ◽  
Author(s):  
Jia Liu ◽  
Michael D. Miller ◽  
Robert M. Danovich ◽  
Nathan Vandergrift ◽  
Fangping Cai ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Treatment Failure ◽  
Low Frequency ◽  
Hiv Treatment ◽  
Viral Population ◽  
Virologic Suppression ◽  
Resistance Mutations ◽  
The Difference ◽  
Allele Specific Sequencing ◽  
Hiv 1

ABSTRACTRaltegravir is highly efficacious in the treatment of HIV-1 infection. The prevalence and impact on virologic outcome of low-frequency resistant mutations among HIV-1-infected patients not previously treated with raltegravir have not been fully established. Samples from HIV treatment-experienced patients entering a clinical trial of raltegravir treatment were analyzed using a parallel allele-specific sequencing (PASS) assay that assessed six primary and six secondary integrase mutations. Patients who achieved and sustained virologic suppression (success patients,n= 36) and those who experienced virologic rebound (failure patients,n= 35) were compared. Patients who experienced treatment failure had twice as many raltegravir-associated resistance mutations prior to initiating treatment as those who achieved sustained virologic success, but the difference was not statistically significant. The frequency of nearly all detected resistance mutations was less than 1% of viral population, and the frequencies of mutations between the success and failure groups were similar. Expansion of pre-existing mutations (one primary and five secondary) was observed in 16 treatment failure patients in whom minority resistant mutations were detected at baseline, suggesting that they might play a role in the development of drug resistance. Two or more mutations were found in 13 patients (18.3%), but multiple mutations were not present in any single viral genome by linkage analysis. Our study demonstrates that low-frequency primary RAL-resistant mutations were uncommon, while minority secondary RAL-resistant mutations were more frequently detected in patients naïve to raltegravir. Additional studies in larger populations are warranted to fully understand the clinical implications of these mutations.

scholarly journals Magnetic Normal Mode Calculations in Big Systems: A Highly Scalable Dynamical Matrix Approach Applied to a Fibonacci-Distorted Artificial Spin Ice

2021 ◽  
Vol 7 (3) ◽  
pp. 34
Author(s):  
Loris Giovannini ◽  
Barry W. Farmer ◽  
Justin S. Woods ◽  
Ali Frotanpour ◽  
Lance E. De Long ◽  
...  
Keyword(s):  
Normal Modes ◽  
Low Frequency ◽  
Fibonacci Sequence ◽  
Exchange Interactions ◽  
Geometric Distortion ◽  
Dynamical Matrix ◽  
Spin Ice ◽  
Magnetization Dynamics ◽  
Distortion Parameter ◽  
Artificial Spin Ice

We present a new formulation of the dynamical matrix method for computing the magnetic normal modes of a large system, resulting in a highly scalable approach. The motion equation, which takes into account external field, dipolar and ferromagnetic exchange interactions, is rewritten in the form of a generalized eigenvalue problem without any additional approximation. For its numerical implementation several solvers have been explored, along with preconditioning methods. This reformulation was conceived to extend the study of magnetization dynamics to a broader class of finer-mesh systems, such as three-dimensional, irregular or defective structures, which in recent times raised the interest among researchers. To test its effectiveness, we applied the method to investigate the magnetization dynamics of a hexagonal artificial spin-ice as a function of a geometric distortion parameter following the Fibonacci sequence. We found several important features characterizing the low frequency spin modes as the geometric distortion is gradually increased.

scholarly journals Meteorological conditions over Antarctic blue-ice areas and their influence on the local surface mass balance

2001 ◽  
Vol 47 (156) ◽  
pp. 37-50 ◽  
Author(s):  
Richard Bintanja ◽  
Carleen H. Reijmer
Keyword(s):  
Mass Balance ◽  
Low Frequency ◽  
Meteorological Conditions ◽  
Surface Mass Balance ◽  
Surface Mass ◽  
Wind Speeds ◽  
Dry Conditions ◽  
The Difference ◽  
Sublimation Rates ◽  
Different Characteristics

AbstractThis paper addresses the causes of the prevailing meteorological conditions observed over an Antarctic blue-ice area and their effect on the surface mass balance. Over blue-ice areas, net accumulation is zero and ablation occurs mainly through sublimation. Sublimation rates are much higher than over adjacent snowfields. The meteorological conditions favourable for high sublimation rates (warm, dry and gusty) are due to the specific orographic setting of this blue-ice area, with usually a steep upwind mountainous slope causing strong adiabatic heating. Diabatic warming due to radiation, and entrainment of warm air from aloft into the boundary layer augment the warming. The prevailing warm, dry conditions explain roughly 50% of the difference in sublimation, and the different characteristics of blue ice (mainly its lower albedo) the other 50%. Most of the annual sublimation (∼70%) takes place during the short summer (mainly in daytime), with winter ablation being restricted to occasional warm, dry föhn-like events. The additional moisture is effectively removed by entrainment and horizontal advection, which are maximum over the blue-ice area. Low-frequency turbulent motions induced by the upwind mountains enhance the vertical turbulent transports. Strong gusts and high peak wind speeds over blue-ice areas cause high potential snowdrift transports, which can easily remove the total precipitation, thereby maintaining zero accumulation.

Spectral broadening of the Soret band in myoglobin: an interpretation by the full spectrum of low-frequency modes from a normal modes analysis

2005 ◽  
Vol 34 (7) ◽  
pp. 881-889 ◽  
Author(s):  
Antonio Cupane ◽  
Marco Cammarata ◽  
Lorenzo Cordone ◽  
Maurizio Leone ◽  
Eugenio Vitrano ◽  
...  
Keyword(s):  
Normal Modes ◽  
Low Frequency ◽  
Soret Band ◽  
Spectral Broadening ◽  
Full Spectrum ◽  
Normal Modes Analysis

Dynamics of Ferroelectric and Nematic Liquid Crystals Confined in Porous Matrices

1994 ◽  
Vol 366 ◽  
Author(s):  
Fouad M. Aliev
Keyword(s):  
Liquid Crystals ◽  
Heterogeneous Media ◽  
Volume Fraction ◽  
Low Frequency ◽  
Pore Wall ◽  
Polar Molecules ◽  
Average Pore ◽  
Surface Polarization ◽  
The Difference ◽  
Frequency Relaxation

ABSTRACTWe performed dielectric spectroscopy measurements to study dynamics of collective modes of ferroelectric (FLC) and molecular motion of nematic (NLC) liquid crystals with polar molecules confined in silica macroporous and microporous glasses with average pore sizes of 1000 Å (volume fraction of pores 40%) and 100 Å (27%) respectively. For FLC the Goldstone and the soft modes are found in macropores. The rotational viscosity associated with the soft mode is about 10 times higher in pores than in the bulk. These modes are not detected in micropores although low frequency relaxation is present. The last one probably is not connected with the nature of liquid crystal but is associated with surface polarization effects typical for two component heterogeneous media. The difference between the dynamics of orientational motion of the polar molecules of NLC in confined geometries and in the bulk is qualitatively determined by the total energy Fs of the interaction between molecules and the surface of the pore wall, which is found Fs ≈ 102erg/cm2.

High-frequency seismic noise as a function of depth

1991 ◽  
Vol 81 (4) ◽  
pp. 1101-1114
Author(s):  
Jerry A. Carter ◽  
Noel Barstow ◽  
Paul W. Pomeroy ◽  
Eric P. Chael ◽  
Patrick J. Leahy
Keyword(s):  
New York ◽  
High Frequency ◽  
Seismic Noise ◽  
Low Frequency ◽  
Time Variability ◽  
Orthogonal Components ◽  
The Difference ◽  
Frequency Coherence ◽  
Cultural Noise ◽  
Natural Wind

Abstract Evidence is presented supporting the view that high-frequency seismic noise decreases with increased depth. Noise amplitudes are higher near the free surface where surface-wave noise, cultural noise, and natural (wind-induced) noise predominate. Data were gathered at a hard-rock site in the northwestern Adirondack lowlands of northern New York. Between 15- and 40-Hz noise levels at this site are more than 10 dB less at 945-m depth than they are at the surface, and from 40 to 100 Hz the difference is more than 20 dB. In addition, time variability of the spectra is shown to be greater at the surface than at either 335- or 945-m depths. Part of the difference between the surface and subsurface noise variability may be related to wind-induced noise. Coherency measurements between orthogonal components of motion show high-frequency seismic noise is more highly organized at the surface than it is at depth. Coherency measurements between the same component of motion at different vertical offsets show a strong low-frequency coherence at least up to 945-m vertical offsets. As the vertical offset decreases, the frequency band of high coherence increases.

scholarly journals Water level oscillations in Monterey Bay and Harbor

Ocean Science ◽  
2015 ◽  
Vol 11 (3) ◽  
pp. 439-453 ◽  
Author(s):  
J. Park ◽  
W. V. Sweet ◽  
R. Heitsenrether
Keyword(s):  
Water Level ◽  
Wave Energy ◽  
Normal Modes ◽  
Low Frequency ◽  
Water Levels ◽  
Level Data ◽  
Modal Amplitude ◽  
Primary Driver ◽  
Potential Mode ◽  
Offshore Wave

Abstract. Seiches are normal modes of water bodies responding to geophysical forcings with potential to significantly impact ecology and maritime operations. Analysis of high-frequency (1 Hz) water level data in Monterey, California, identifies harbor modes between 10 and 120 s that are attributed to specific geographic features. It is found that modal amplitude modulation arises from cross-modal interaction and that offshore wave energy is a primary driver of these modes. Synchronous coupling between modes is observed to significantly impact dynamic water levels. At lower frequencies with periods between 15 and 60 min, modes are independent of offshore wave energy, yet are continuously present. This is unexpected since seiches normally dissipate after cessation of the driving force, indicating an unknown forcing. Spectral and kinematic estimates of these low-frequency oscillations support the idea that a persistent anticyclonic mesoscale gyre adjacent to the bay is a potential mode driver, while discounting other sources.

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