scholarly journals FF12MC: A revised AMBER forcefield and new protein simulation protocol

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Md Simulations ◽  
General Purpose ◽  
Protein Simulation ◽  
Simulation Protocol ◽  
Left And Right ◽  
Experimental Values ◽  
The Right ◽  
Protein Models ◽  
Explicit Solvation ◽  
New Protein

ABSTRACTSpecialized to simulate proteins in molecular dynamics (MD) simulations with explicit solvation, FF12MC is a combination of a new protein simulation protocol employing uniformly reduced atomic masses by tenfold and a revised AMBER forcefield FF99 with (i) shortened CH bonds, (ii) removal of torsions involving a nonperipheralsp3atom, and (iii) reduced 1-4 interaction scaling factors of torsionsϕandψThis article reports that in multiple, distinct, independent, unrestricted, unbiased, isobaric-isothermal, and classical MD simulations FF12MC can (i) simulate the experimentally observed flipping between left-and right-handed configurations for C14-C38 of BPTI in solution, (ii) autonomously fold chignolin, CLN025, and Trp-cage with folding times that agree with the experimental values, (iii) simulate subsequent unfolding and refolding of these miniproteins, and (iv) achieve a robust Z score of 1.33 for refining protein models TMR01, TMR04, and TMR07. By comparison, the latest general-purpose AMBER forcefield FF14SB locks the C14-C38 bond to the right-handed configuration in solution under the same protein simulation conditions. Statistical survival analysis shows that FF12MC folds chignolin and CLN025 in isobaric-isothermal MD simulations 2-4 times faster than FF14SB under the same protein simulation conditions. These results suggest that FF12MC may be used for protein simulations to study kinetics and thermodynamics of miniprotein folding as well as protein structure and dynamics.

Separable Mechanisms in Face Processing: Evidence from Hemispheric Specialization

1991 ◽  
Vol 3 (1) ◽  
pp. 42-58 ◽  
Author(s):  
Lynn A. Hillger ◽  
Olivier Koenig
Keyword(s):  
Left Hemisphere ◽  
Face Processing ◽  
Visual Processing ◽  
Right Hemisphere ◽  
Hemispheric Specialization ◽  
Facial Feature ◽  
General Purpose ◽  
Facial Features ◽  
Left And Right ◽  
The Right

This article addresses three issues in face processing: First, is face processing primarily accomplished by the right hemisphere, or do both left- and right-hemisphere mechanisms play important roles? Second, are the mechanisms the same as those involved in general visual processing, or are they dedicated to face processing? Third, how can the mechanisms be characterized more precisely in terms of processes such as visual parsing? We explored these issues using the divided visual field methodology in four experiments. Experiments 1 and 2 provided evidence that both left- and right-hemisphere mechanisms are involved in face processing. In Experiment 1, a right-hemisphere advantage was found for both Same and Different trials when Same faces were identical and Different faces differed on all three internal facial features. Experiment 2 replicated the right-hemisphere advantage for Same trials but showed a left-hemisphere advantage for Different trials when one of three facial features differed between the target and the probe faces. Experiment 3 showed that the right-hemisphere advantage obtained with upright faces in Experiment 2 disappeared when the faces were inverted. This result suggests that there are right-hemisphere mechanisms specialized for processing upright faces, although it could not be determined whether these mechanisms are completely face-specific. Experiment 3 also provided evidence that the left-hemisphere mechanisms utilized in face processing tasks are general-purpose visual mechanisms not restricted to particular classes of visual stimuli. In Experiment 4, a left-hemisphere advantage was obtained when the task was to find one facial feature that was the same between the target and the probe faces. We suggest that left-hemisphere advantages shown in face processing are due to the parsing and analysis of the local elements of a face.

Comparison of the efficiency of the indexes of Pont and Korkhause with Kernott technique in patients with narrowing of maxilla

2020 ◽  
Vol 20 (3) ◽  
pp. 199-203
Author(s):  
O. I. Admakin ◽  
I. A. Solop ◽  
A. D. Oksentyuk
Keyword(s):  
Dental Treatment ◽  
Standard Analysis ◽  
Clinical Hospital ◽  
Control Models ◽  
Diagnostic Models ◽  
Left And Right ◽  
The Asymmetry ◽  
The Right ◽  
The University ◽  
Medical University

Relevance. The narrowing of the maxilla is one of the most common pathologies in orthodontics. Recent studies show that the narrowing is always asymmetric which is connected to the rotation of the maxilla. To choose the treatment correctly one need a calculation that reveals the asymmetry, which is impossible with using standard indexes.Purpose – to compare efficiency of indexes of Pont and Korkhause with the Kernott's method in patients with narrowing of the maxilla.Materials and methods. The study involved 35 children aged from 8 to 12 years old undergoing dental treatment in the University Children's Clinical Hospital of the First Moscow State Medical University with no comorbidities. For every patient a gypsum model was prepared and after that to carry out the biometrical calculation. In this study two indexes were used: Pont's index and Korkhause's; using this standard analysis the narrowing of the maxilla was revealed. After using Pont's Index and Korkhaus analysis all the models were calculated by the method of Kernott with Kernott's dynamic pentagon.Results. As a result of the analysis of the control diagnostic models a narrowing of the maxilla in 69% of cases (n = 24) was revealed in all cases, the deviation of the size of the dentition was asymmetric. Thus, 65% of the surveyed models showed a narrowing on the right. This narrowing was of a different severity and averaged 15 control models.Conclusions. This shows that for the biometrics of diagnostic models it is necessary to use methods that allow to estimate the width of the dentition rows on the left and on the right separately. To correct the asymmetric narrowing of the dentition, it is preferable to use non-classical expanding devices that act equally on the left and right sides separetly.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

scholarly journals Transcriptomic uniqueness and commonality of the ion channels and transporters in the four heart chambers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sanda Iacobas ◽  
Bogdan Amuzescu ◽  
Dumitru A. Iacobas
Keyword(s):  
Ion Channels ◽  
Cycle Phase ◽  
Functional Roles ◽  
Expression Control ◽  
Gene Expression Control ◽  
Left And Right ◽  
The Right ◽  
Phase Out ◽  
Right Atria ◽  
Agilent Microarrays

AbstractMyocardium transcriptomes of left and right atria and ventricles from four adult male C57Bl/6j mice were profiled with Agilent microarrays to identify the differences responsible for the distinct functional roles of the four heart chambers. Female mice were not investigated owing to their transcriptome dependence on the estrous cycle phase. Out of the quantified 16,886 unigenes, 15.76% on the left side and 16.5% on the right side exhibited differential expression between the atrium and the ventricle, while 5.8% of genes were differently expressed between the two atria and only 1.2% between the two ventricles. The study revealed also chamber differences in gene expression control and coordination. We analyzed ion channels and transporters, and genes within the cardiac muscle contraction, oxidative phosphorylation, glycolysis/gluconeogenesis, calcium and adrenergic signaling pathways. Interestingly, while expression of Ank2 oscillates in phase with all 27 quantified binding partners in the left ventricle, the percentage of in-phase oscillating partners of Ank2 is 15% and 37% in the left and right atria and 74% in the right ventricle. The analysis indicated high interventricular synchrony of the ion channels expressions and the substantially lower synchrony between the two atria and between the atrium and the ventricle from the same side.

The role of visual experience for spatial numerical associations

2012 ◽  
Vol 25 (0) ◽  
pp. 222 ◽  
Author(s):  
Michael J. Proulx ◽  
Achille Pasqualotto ◽  
Shuichiro Taya
Keyword(s):  
Visual Experience ◽  
Opposite Effect ◽  
Random Number Generation ◽  
Number Line ◽  
Mental Number Line ◽  
Generation Task ◽  
Congenitally Blind ◽  
Left And Right ◽  
The Right

The topographic representation of space interacts with the mental representation of number. Evidence for such number–space relations have been reported in both synaesthetic and non-synaesthetic participants. Thus far most studies have only examined related effects in sighted participants. For example, the mental number line increases in magnitude from left to right in sighted individuals (Loetscher et al., 2008, Curr. Biol.). What is unclear is whether this association arises from innate mechanisms or requires visual experience early in life to develop in this way. Here we investigated the role of visual experience for the left to right spatial numerical association using a random number generation task in congenitally blind, late blind, and blindfolded sighted participants. Participants orally generated numbers randomly whilst turning their head to the left and right. Sighted participants generated smaller numbers when they turned their head to the left than to the right, consistent with past results. In contrast, congenitally blind participants generated smaller numbers when they turned their head to the right than to the left, exhibiting the opposite effect. The results of the late blind participants showed an intermediate profile between that of the sighted and congenitally blind participants. Visual experience early in life is therefore necessary for the development of the spatial numerical association of the mental number line.

scholarly journals Surface Evolution During Semiconductor Processing

VLSI Design ◽  
1998 ◽  
Vol 6 (1-4) ◽  
pp. 379-384 ◽  
Author(s):  
Ganesh Rajagopalan ◽  
Vadali Mahadev ◽  
Timothy S. Cale
Keyword(s):  
Riemann Problem ◽  
Surface Profile ◽  
Numerical Implementation ◽  
Jump Conditions ◽  
Semiconductor Processing ◽  
Explicit Integration ◽  
Surface Evolution ◽  
Left And Right ◽  
The Right ◽  
Surface Angle

We discuss our approach to using the Riemann problem to compute surface profile evolution during the simulation of deposition, etch and reflow processes. Each pair of segments which represents the surface is processed sequentially. For cases in which both segments are the same material, the Riemann problem is solved. For cases in which the two segments are different materials, two Riemann problems are solved. The material boundary is treated as the right segment for the left material and as the left segment for the right material. The critical equations for the analyses are the characteristics of the Riemann problem and the ‘jump conditions’ which represent continuity of the surface. Examples are presented to demonstrate selected situations. One limitation of the approach is that the velocity of the surface is not known as a function of the surface angle. Rather, it is known for the angles of the left and right segments. The rate as a function of angle must be assumed for the explicit integration procedure used. Numerical implementation is briefly discussed.

scholarly journals Towards an accurate description of perovskite ferroelectrics: exchange and correlation effects

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Simuck F. Yuk ◽  
Krishna Chaitanya Pitike ◽  
Serge M. Nakhmanson ◽  
Markus Eisenbach ◽  
Ying Wai Li ◽  
...  
Keyword(s):  
Density Functional ◽  
General Purpose ◽  
Correlation Effects ◽  
Lattice Constants ◽  
Bulk Solids ◽  
Wide Range ◽  
Exchange Enhancement ◽  
Experimental Values ◽  
Similar Accuracy ◽  
Ferroelectric Oxides

Abstract Using the van der Waals density functional with C09 exchange (vdW-DF-C09), which has been applied to describing a wide range of dispersion-bound systems, we explore the physical properties of prototypical ABO 3 bulk ferroelectric oxides. Surprisingly, vdW-DF-C09 provides a superior description of experimental values for lattice constants, polarization and bulk moduli, exhibiting similar accuracy to the modified Perdew-Burke-Erzenhoff functional which was designed specifically for bulk solids (PBEsol). The relative performance of vdW-DF-C09 is strongly linked to the form of the exchange enhancement factor which, like PBEsol, tends to behave like the gradient expansion approximation for small reduced gradients. These results suggest the general-purpose nature of the class of vdW-DF functionals, with particular consequences for predicting material functionality across dense and sparse matter regimes.

scholarly journals Ventilation/perfusion mismatch during lung aeration at birth

2014 ◽  
Vol 117 (5) ◽  
pp. 535-543 ◽  
Author(s):  
Justin A. R. Lang ◽  
James T. Pearson ◽  
Arjan B. te Pas ◽  
Megan J. Wallace ◽  
Melissa L. Siew ◽  
...  
Keyword(s):  
Pulmonary Arteries ◽  
Left Lung ◽  
X Ray ◽  
Lung Aeration ◽  
X Ray Imaging ◽  
Iodine Level ◽  
Pulmonary Shunting ◽  
Left And Right ◽  
Near Term ◽  
The Right

At birth, the transition to newborn life is triggered by lung aeration, which stimulates a large increase in pulmonary blood flow (PBF). Current theories predict that the increase in PBF is spatially related to ventilated lung regions as they aerate after birth. Using simultaneous phase-contrast X-ray imaging and angiography we investigated the spatial relationships between lung aeration and the increase in PBF after birth. Six near-term (30-day gestation) rabbits were delivered by caesarean section, intubated and an intravenous catheter inserted, before they were positioned for X-ray imaging. During imaging, iodine was injected before ventilation onset, after ventilation of the right lung only, and after ventilation of both lungs. Unilateral ventilation increased iodine levels entering both left and right pulmonary arteries (PAs) and significantly increased heart rate, iodine ejection per beat, diameters of both left and right PAs, and number of visible vessels in both lungs. Within the 6th intercostal space, the mean gray level (relative measure of iodine level) increased from 68.3 ± 11.6 and 70.3 ± 7.5%·s to 136.3 ± 22.6 and 136.3 ± 23.7%·s in the left and right PAs, respectively. No differences were observed between vessels in the left and right lungs, despite the left lung not initially being ventilated. The increase in PBF at birth is not spatially related to lung aeration allowing a large ventilation/perfusion mismatch, or pulmonary shunting, to occur in the partially aerated lung at birth.

Handedness affects Emotional Valence Asymmetry

1989 ◽  
Vol 68 (2) ◽  
pp. 435-441 ◽  
Author(s):  
Richard A. McFarland ◽  
Robert Kennison
Keyword(s):  
Negative Affect ◽  
Hemispheric Asymmetry ◽  
Emotional Responses ◽  
Emotional Valence ◽  
Left Handed ◽  
Two Factors ◽  
Left And Right ◽  
The Asymmetry ◽  
The Right ◽  
Cerebral Processing

Music was played monaurally to 80 right-handed and 80 left-handed subjects. Right-handers reported more positive and less negative affect if the music was to the right ear. Left-handers reported experiencing more positive and less negative affect during music to the left ear. The hand × ear interaction was significant. The valence of emotional responses to the music seems influenced by a combination of at least two factors, (1) differences between left- and right-handers in the cerebral processing of emotional valence and (2) differences in the processing of emotional valence within each handedness group depending upon which hemisphere was initially most strongly engaged by the music. These results partially corroborate and extend the findings of previous studies in which briefer stimuli were presented tachistoscopically or dichotically. It is concluded that, while there is hemispheric asymmetry in the processing of emotional valence, the direction of the asymmetry may be associated with the handedness of the subjects.

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