Introducing the ELF Topological Analysis in the Field of Quasirelativistic Quantum Calculations

Quantum calculations on 976 atoms of the voltage sensing domain of the Kv1.2 channel, with protons in several positions, give energy, charge transfer, and other properties. Motion of the S4 transmembrane segment that accounts for gating current in standard models is shown not to occur; there is H+ transfer instead. The potential at which two proton positions cross in energy approximately corresponds to the gating potential for the channel. The charge displacement seems approximately correct for the gating current. Two mutations are accounted for (Y266F, R300cit, cit =citrulline). The primary conclusion is that voltage sensing depends on H+ transfer, not motion of arginine charges.

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DIMENSIONING OF THE FRONTAL SUSPENSION SYSTEM OF THE DOUBLE-A TYPE THROUGH TOPOLOGICAL ANALYSIS.

10.26678/abcm.cobem2017.cob17-1986 ◽

2017 ◽

Author(s):

Tiago Ferreira ◽

Thiago Moreira ◽

Gustavo Melchiades ◽

Lucas Ferreira ◽

Diógenes Sena de França e Silva

Keyword(s):

Topological Analysis ◽

Suspension System

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Topological analysis of hydrogen bonding in protein structure

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1990.tb15412.x ◽

1990 ◽

Vol 188 (2) ◽

pp. 361-365 ◽

Cited By ~ 8

Author(s):

Boryeu MAO ◽

Kuo-Chen CHOU ◽

Gerald M. MAGGIORA

Keyword(s):

Hydrogen Bonding ◽

Protein Structure ◽

Topological Analysis

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Quantum Calculations on Ion Channels: Why Are They More Useful Than Classical Calculations, and for Which Processes Are They Essential?

Symmetry ◽

10.3390/sym13040655 ◽

2021 ◽

Vol 13 (4) ◽

pp. 655

Author(s):

Alisher M. Kariev ◽

Michael E. Green

Keyword(s):

Charge Transfer ◽

Ion Channels ◽

Correlation Energy ◽

Force Fields ◽

Critical Role ◽

Atomic Scale ◽

Quantum Calculations ◽

Interatomic Distances ◽

Classical Analogue ◽

Exchange And Correlation

There are reasons to consider quantum calculations to be necessary for ion channels, for two types of reasons. The calculations must account for charge transfer, and the possible switching of hydrogen bonds, which are very difficult with classical force fields. Without understanding charge transfer and hydrogen bonding in detail, the channel cannot be understood. Thus, although classical approximations to the correct force fields are possible, they are unable to reproduce at least some details of the behavior of a system that has atomic scale. However, there is a second class of effects that is essentially quantum mechanical. There are two types of such phenomena: exchange and correlation energies, which have no classical analogues, and tunneling. Tunneling, an intrinsically quantum phenomenon, may well play a critical role in initiating a proton cascade critical to gating. As there is no classical analogue of tunneling, this cannot be approximated classically. Finally, there are energy terms, exchange and correlation energy, whose values can be approximated classically, but these approximations must be subsumed within classical terms, and as a result, will not have the correct dependence on interatomic distances. Charge transfer, and tunneling, require quantum calculations for ion channels. Some results of quantum calculations are shown.

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Exploring the predictive value of lesion topology on motor function outcomes in a porcine ischemic stroke model

Scientific Reports ◽

10.1038/s41598-021-83432-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kelly M. Scheulin ◽

Brian J. Jurgielewicz ◽

Samantha E. Spellicy ◽

Elizabeth S. Waters ◽

Emily W. Baker ◽

...

Keyword(s):

Motor Function ◽

Pearson Correlation ◽

Topological Analysis ◽

Brain Atlas ◽

Analysis Approach ◽

Lesion Volume ◽

Stroke Outcomes ◽

Correlation Analyses ◽

Diagnostic Potential ◽

Functional Gait

AbstractHarnessing the maximum diagnostic potential of magnetic resonance imaging (MRI) by including stroke lesion location in relation to specific structures that are associated with particular functions will likely increase the potential to predict functional deficit type, severity, and recovery in stroke patients. This exploratory study aims to identify key structures lesioned by a middle cerebral artery occlusion (MCAO) that impact stroke recovery and to strengthen the predictive capacity of neuroimaging techniques that characterize stroke outcomes in a translational porcine model. Clinically relevant MRI measures showed significant lesion volumes, midline shifts, and decreased white matter integrity post-MCAO. Using a pig brain atlas, damaged brain structures included the insular cortex, somatosensory cortices, temporal gyri, claustrum, and visual cortices, among others. MCAO resulted in severely impaired spatiotemporal gait parameters, decreased voluntary movement in open field testing, and higher modified Rankin Scale scores at acute timepoints. Pearson correlation analyses at acute timepoints between standard MRI metrics (e.g., lesion volume) and functional outcomes displayed moderate R values to functional gait outcomes. Moreover, Pearson correlation analyses showed higher R values between functional gait deficits and increased lesioning of structures associated with motor function, such as the putamen, globus pallidus, and primary somatosensory cortex. This correlation analysis approach helped identify neuroanatomical structures predictive of stroke outcomes and may lead to the translation of this topological analysis approach from preclinical stroke assessment to a clinical biomarker.

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Quantum calculations of the photoelectron spectra of the OH−·NH3 anion: implications for OH + NH3 → H2O + NH2 reaction dynamics

Physical Chemistry Chemical Physics ◽

10.1039/d0cp06514e ◽

2021 ◽

Vol 23 (11) ◽

pp. 6950-6958

Author(s):

Kohei Saito ◽

Yutaro Sugiura ◽

Takaaki Miyazaki ◽

Yukinobu Takahashi ◽

Toshiyuki Takayanagi

Keyword(s):

Quantum Dynamics ◽

Photoelectron Spectrum ◽

Reaction Dynamics ◽

Photoelectron Spectra ◽

Quantum Calculations ◽

Anion Complex

Quantum dynamics calculations were performed to analyze the experimentally measured photoelectron spectrum of the OH−·NH3 anion complex.

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Data Parallel Hypersweeps for in Situ Topological Analysis

2020 IEEE 10th Symposium on Large Data Analysis and Visualization (LDAV) ◽

10.1109/ldav51489.2020.00008 ◽

2020 ◽

Author(s):

Petar Hristov ◽

Gunther H. Weber ◽

Hamish A. Carr ◽

Oliver Rubel ◽

James P. Ahrens

Keyword(s):

Topological Analysis ◽

Data Parallel

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