scholarly journals Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics programDivConinto thePHENIXrefinement package

2014 ◽  
Vol 70 (5) ◽  
pp. 1233-1247 ◽  
Author(s):  
Oleg Y. Borbulevych ◽  
Joshua A. Plumley ◽  
Roger I. Martin ◽  
Kenneth M. Merz ◽  
Lance M. Westerhoff
Keyword(s):  
Quantum Mechanics ◽  
A Priori ◽  
Data Bank ◽  
Linear Scaling ◽  
X Ray ◽  
Energy Functionals ◽  
The Past ◽  
Single Structure ◽  
Potential Ligand ◽  
High Throughput Crystallography

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requiresa prioriunderstanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) programDivConwith thePHENIXX-ray refinement engine. ThePHENIX/DivConpackage has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years.PHENIX/DivCondoes not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as manya prioriassumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating thatPHENIX/DivConis applicable to both single-structure and high-throughput crystallography.

Aristotle and Hegel on Nature: Some Similarities

1992 ◽  
Vol 13 (02) ◽  
pp. 13-29
Author(s):  
Liberato Santoro-Brienza
Keyword(s):  
Quantum Mechanics ◽  
Genetic Engineering ◽  
A Priori ◽  
Considerable Degree ◽  
Western Philosophy ◽  
Philosophy Of Nature ◽  
The Past

Michael Petry has observed that “until 1970 there was nobody among the hegelians, not to mention the philosophers of the Naturwissenschaften, willing to recognise Hegel's philosophy of nature as an area of investigation to be taken seriously.” An analogous fate seems to have afflicted Aristotle's Physics, if one agrees with Heidegger that: “The Aristotelian Physics is the arcane (verborgene) fundamental book of Western philosophy and, insofar as arcane, it has never been studied sufficiently.” Fortunately, the past neglect has been amply compensated for by the considerable degree of interest shown, in more recent years, towards both Hegel's and Aristotle's philosophy of nature. With reference to Hegel, that interest may have been nourished initially by the recognition of some isomorphic traits obtaining in Hegel's doctrine and in the methodology of structuralism and gestaltism. Furthermore, part of that interest must have also been triggered by the overall state of bankruptcy and disrepute which have befallen mechanistic, quantitative, empirical or neo-empirical and neo-positivist explanations of reality and of nature. Think of the developments of genetic biology, pathology and genetic engineering. Quantum Mechanics, the highly speculative turn in physics, cosmology, mathematics. By now, the assumptions, methods and findings of these sciences seem to be more kin to Aristotle and Hegel than to Newton and Galileo. Other hypothetical reasons could be offered, to explain the renewed attention paid to Hegel's philosophy of nature. One point, to begin with, emerges from the panorama of recent research on Hegel, namely that - regardless of and despite the recurrent mythical, hyper-animistic, anthropomorphic images, sustained by analogies and metaphorical diction; also despite of the frequent obscurities and downright factual mistakes - the philosopher cannot be sweepingly accused of scientific ignorance, nor of endemically gratuituous a priori, abstract reflection.

A Constant Proportion in Protein Structure

2018 ◽  
Author(s):  
Francisco Javier Lobo-Cabrera
Keyword(s):  
Protein Structure ◽  
Spatial Clustering ◽  
A Priori ◽  
Data Bank ◽  
X Ray ◽  
Protein Size ◽  
Protein Prediction ◽  
Quality Check ◽  
First Time ◽  
Secondary Structure Composition

The principles governing protein structure are largely unknown. Here, a structural proportion universal (R2 = 0.978) among proteins is reported. The model variance is shown to be independent from protein size, secondary structure composition, compactness or relative surface area. The structural characteristic under study --named here QUILLO-- quantifies residue-type spatial clustering. In this way, polar, hydrophobic, acidic and basic residues are evaluated individually and their values added up. For the analysis, all X-Ray currently determined structures deposited in the Protein Data Bank were studied. The QUILLO proportion offers for the first time an a priori protein prediction quality-check. Indeed, predictions with unexpected proportion values correspond to low ranks in the CASP12 experiment. The reason behind a specific, constant rule for protein folding remains unknown.

The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

1973 ◽  
Vol 31 ◽  
pp. 132-133 ◽  
Author(s):  
R. E. Herfert
Keyword(s):  
Surface Characterization ◽  
Analytical Techniques ◽  
X Ray Diffraction ◽  
Depth Of Penetration ◽  
X Ray ◽  
The Past ◽  
Transmission Electron ◽  
Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

RNA polymerase: Preparation and structural analysis of helical polymers

1984 ◽  
Vol 42 ◽  
pp. 152-153
Author(s):  
E. Loren Buhle ◽  
Pamela Rew ◽  
Ueli Aebi
Keyword(s):  
Structural Analysis ◽  
Rna Polymerase ◽  
Molecular Level ◽  
X Ray Diffraction ◽  
Helical Polymers ◽  
X Ray ◽  
E Coli ◽  
The Past ◽  
Ordered Arrays ◽  
Low Ionic Strength

While DNA-dependent RNA polymerase represents one of the key enzymes involved in transcription and ultimately in gene expression in procaryotic and eucaryotic cells, little progress has been made towards elucidation of its 3-D structure at the molecular level over the past few years. This is mainly because to date no 3-D crystals suitable for X-ray diffraction analysis have been obtained with this rather large (MW ~500 kd) multi-subunit (α2ββ'ζ). As an alternative, we have been trying to form ordered arrays of RNA polymerase from E. coli suitable for structural analysis in the electron microscope combined with image processing. Here we report about helical polymers induced from holoenzyme (α2ββ'ζ) at low ionic strength with 5-7 mM MnCl2 (see Fig. 1a). The presence of the ζ-subunit (MW 86 kd) is required to form these polymers, since the core enzyme (α2ββ') does fail to assemble into such structures under these conditions.

scholarly journals The internal conversion of gamma-rays.—Part II

1928 ◽  
Vol 121 (787) ◽  
pp. 447-456
Keyword(s):  
Magnetic Field ◽  
Quantum Mechanics ◽  
Wave Equation ◽  
Gamma Rays ◽  
Internal Conversion ◽  
Scalar Potential ◽  
X Ray ◽  
Electro Magnetic Field ◽  
Γ Rays ◽  
Electro Magnetic

In a previous paper the absorption of γ-rays in the K-X-ray levels of the atom in which they are emitted was calculated according to the Quantum Mechanics, supposing the γ-rays to be emitted from a doublet of moment f ( t ) at the centre of the atom. The non-relativity wave equation derived from the relativity wave equation for an electron of charge — ε moving in an electro-magnetic field of vector potential K and scalar potential V is h 2 ∇ 2 ϕ + 2μ ( ih ∂/∂ t + εV + ih ε/μ c (K. grad)) ϕ = 0. (1) Suppose, however, that K involves the space co-ordinates. Then, (K. grad) ϕ ≠ (grad . K) ϕ , and the expression (K . grad) ϕ is not Hermitic. Equation (1) cannot therefore be the correct non-relativity wave equation for a single electron in an electron agnetic field, and we must substitute h 2 ∇ 2 ϕ + 2μ ( ih ∂/∂ t + εV) ϕ + ih ε/ c ((K. grad) ϕ + (grad. K) ϕ ) = 0. (2)

scholarly journals Workload for radiologists during on-call hours: dramatic increase in the past 15 years

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
R. J. M. Bruls ◽  
R. M. Kwee
Keyword(s):  
Western Europe ◽  
Kendall Test ◽  
Kendall’S Tau ◽  
Kendall's Tau ◽  
X Ray ◽  
The Past ◽  
Relative Value ◽  
Burn Out ◽  
Picture Archiving And Communication ◽  
Ct Studies

Abstract Background The objective of this study is to investigate the workload for radiologists during on-call hours and to quantify the 15-year trend in a large general hospital in Western Europe. Methods Data regarding the number of X-ray, ultrasound and computed tomography (CT) studies during on-call hours (weekdays between 6.00 p.m. and 7.00 a.m., weekends, and national holidays) between 2006 and 2020 were extracted from the picture archiving and communication system. All studies were converted into relative value units (RVUs) to estimate the on-call workload. The Mann–Kendall test was performed to assess the temporal trend. Results The total RVUs during on-call hours showed a significant increase between 2006 and 2020 (Kendall's tau-b = 0.657, p = 0.001). The overall workload in terms of RVUs during on-call hours has quadrupled. The number of X-ray studies significantly decreased (Kendall's tau-b = − 0.433, p = 0.026), whereas the number of CT studies significantly increased (Kendall's tau-b = 0.875, p < 0.001) between 2006 and 2020. CT studies which increased by more than 500% between 2006 and 2020 are CT for head trauma, brain CTA, brain CTV, chest CT (for suspected pulmonary embolism), spinal CT, neck CT, pelvic CT, and CT for suspected aortic dissection. The number of ultrasound studies did not change significantly (Kendall's tau-b = 0.202, p = 0.298). Conclusions The workload for radiologists during on-call hours increased dramatically in the past 15 years. The growing amount of CT studies is responsible for this increase. Radiologist and technician workforce should be matched to this ongoing increasing trend to avoid potential burn-out and to maintain quality and safety of radiological care.

scholarly journals Turner Syndrome, Uncommonly Diagnosed Cause of Short Stature: Case Report and Review of Literature

2013 ◽  
Vol 33 (1) ◽  
pp. 74-76
Author(s):  
S Basnet ◽  
A Eleena ◽  
AK Sharma
Keyword(s):  
Growth Hormone ◽  
Short Stature ◽  
Turner Syndrome ◽  
Age Estimation ◽  
Bone Age ◽  
Review Of Literature ◽  
X Ray ◽  
Dysmorphic Features ◽  
The Past ◽  
Hormone Analysis

Many children are frequently brought to the paediatric clinic for evaluation of short stature. Evaluation for these children does not go beyond x-ray for bone age estimation and growth hormone analysis. Most of them are considered having constitutional or genetic cause for their short stature. However, shuttle dysmorphic features could be missed in many of them. Hence, many children might be having chromosomal anomaly as an underlying cause. We report a case of 40 months who had been evaluated several times in the past for pneumonia, otitis media and short stature is finally diagnosed to have Turner syndrome. DOI: http://dx.doi.org/10.3126/jnps.v33i1.8174 J Nepal Paediatr Soc. 2013;33(1):74-76

scholarly journals The measure problem in no-collapse (many worlds) quantum mechanics

2017 ◽  
Vol 26 (03) ◽  
pp. 1730008 ◽  
Author(s):  
Stephen D. H. Hsu
Keyword(s):  
Wave Function ◽  
Quantum Mechanics ◽  
Probability Measure ◽  
Ab Initio ◽  
Subjective Probability ◽  
State Vector ◽  
A Priori ◽  
Born Rule ◽  
Many Worlds ◽  
Measure Problem

We explain the measure problem (cf. origin of the Born probability rule) in no-collapse quantum mechanics. Everett defined maverick branches of the state vector as those on which the usual Born probability rule fails to hold — these branches exhibit highly improbable behaviors, including possibly the breakdown of decoherence or even the absence of an emergent semi-classical reality. Derivations of the Born rule which originate in decision theory or subjective probability (i.e. the reasoning of individual observers) do not resolve this problem, because they are circular: they assume, a priori, that the observer occupies a non-maverick branch. An ab initio probability measure is sometimes assumed to explain why we do not occupy a maverick branch. This measure is constrained by, e.g. Gleason’s theorem or envariance to be the usual Hilbert measure. However, this ab initio measure ultimately governs the allocation of a self or a consciousness to a particular branch of the wave function, and hence invokes primitives which lie beyond the Everett wave function and beyond what we usually think of as physics. The significance of this leap has been largely overlooked, but requires serious scrutiny.

Sign in / Sign up

Export Citation Format

Share Document