scholarly journals Predicting Transmembrane (TM) Domain Dimer Structures using Martini 3

2021 ◽  
Author(s):  
Amita R. Sahoo ◽  
Paulo C. T. Souza ◽  
Zhiyuan Meng ◽  
Matthias Buck
Keyword(s):  
Coarse Grain ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Transmembrane Receptors ◽  
Structure And Dynamics ◽  
Intracellular Receptor ◽  
Tm Domain ◽  
Recent Version ◽  
Good Agreement

AbstractDetermination of the structure and dynamics of transmembrane (TM) domains of single-transmembrane receptors is key to understanding their mechanism of signal transduction across the plasma membrane. Although many studies have been performed on isolated soluble extra- and intracellular receptor domains in aqueous solutions, limited knowledge exists on the lipid embedded TM region. In this study, we predict the assembly of alternate configurations of receptor TM domain dimers using the Martini 3 force field for coarse-grain (CG) molecular dynamic simulations. This recent version of Martini has new bead types and sizes, which allows more accurate predictions of molecular packing and interactions compared to the previous version. Our results with Martini 3 simulations show overall good agreement with ab initio predictions using PREDDIMER and with available NMR derived structures for TM helix dimers. Understanding and predicting the association TM domains may help us to better understand the signalling mechanism of TM receptors, in turn providing the opportunity for development of new pharmaceuticals, some of which are peptide based.

Thermoluminescence Dating of Coarse-Grain Quartz from the Malan Loess at Zhaitang Section, China

1987 ◽  
Vol 28 (3) ◽  
pp. 356-363 ◽  
Author(s):  
Lu Yanchou ◽  
A. J. Mortlock ◽  
D. M. Price ◽  
M. L. Readhead
Keyword(s):  
Age Determination ◽  
Total Sample ◽  
Coarse Grain ◽  
Annual Dose ◽  
Fine Grain ◽  
Malan Loess ◽  
Thermoluminescence Dating ◽  
Beijing China ◽  
Good Agreement

AbstractThermoluminescence (TL) ages were obtained for five loess samples taken from the Zhaitang section near Beijing, China, using the coarse-grain quartz technique. The paleodose values have been determined by the method of total sample bleaching and regeneration of the TL growth curve. The method appears to be suitable for the age determination of loess samples up to about 150,000 yr where the annual dose-rate values are of the order 3–4 mGy/yr. This limit is a function of the total accumulated dose. The ages are in good agreement with those obtained by a fine-grain TL technique and are consistent with geological and geomagnetostratigraphic evidence.

Determination of the Structures of Uranyl-Tri-n-butyl-Phosphate Aggregates by Coupling Experimental Results with Molecular Dynamic Simulations

2017 ◽  
Vol 23 (65) ◽  
pp. 16660-16670 ◽  
Author(s):  
Phillipe Guilbaud ◽  
Laurence Berthon ◽  
Wilfried Louisfrema ◽  
Olivier Diat ◽  
Nicole Zorz
Keyword(s):  
Molecular Dynamic ◽  
Experimental Results ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

scholarly journals First-Principles Calculations of Shocked Fluid Helium in Partially Ionized Region

2012 ◽  
Vol 12 (4) ◽  
pp. 1121-1128 ◽  
Author(s):  
Cong Wang ◽  
Xian-Tu He ◽  
Ping Zhang
Keyword(s):  
Equation Of State ◽  
First Principles ◽  
Calculated Data ◽  
Molecular Dynamic Simulations ◽  
First Principles Calculations ◽  
Dynamic Simulations ◽  
Gas Gun ◽  
Atomic Ionization ◽  
Simulation Results ◽  
Good Agreement

AbstractQuantum molecular dynamic simulations have been employed to study the equation of state (EOS) of fluid helium under shock compressions. The principal Hugoniot is determined from EOS, where corrections from atomic ionization are added onto the calculated data. Our simulation results indicate that principal Hugoniot shows good agreement with gas gun and laser driven experiments, and maximum compression ratio of 5.16 is reached at 106 GPa.

COMPARATIVE ACTION OF VARIOUS OESTROGENIC COMPOUNDS ON MOUSE VAGINAL SIALIC ACIDS (II)

1969 ◽  
Vol 62 (4) ◽  
pp. 663-670 ◽  
Author(s):  
Lars Carlborg
Keyword(s):  
Sialic Acid ◽  
Response Curve ◽  
Sialic Acids ◽  
Clear Cut ◽  
Suitable Parameter ◽  
Sufficient Degree ◽  
Comparative Action ◽  
Relative Potencies ◽  
Good Agreement

ABSTRACT Oestrogens administered in lower doses than necessary to induce full cornification of the mouse vagina induce mucification. It was shown previously that the degree of mucification could be estimated by quantitative determination of sialic acids. A suitable parameter for oestrogen assay was the measurement of vaginal sialic acid concentration which exhibited a clear cut dose response curve. Eleven assays of various oestrogens were performed with this method. Their estimated relative potencies were in good agreement with other routine oestrogen assays. A statistically sufficient degree of precision was found. The sensitivity was of the same order, or slightly higher, than the Allen-Doisy test.

ІНТЕРПРЕТАЦІЯ КАТЕГОРІЇ РОЗВИТКУ В СУЧАСНІЙ ПСИХОЛОГІЇ

1970 ◽  
Vol 8 (1) ◽  
pp. 22-30
Author(s):  
Анжеліка Шамне
Keyword(s):  
Cultural Context ◽  
Developmental Psychology ◽  
Structure And Dynamics ◽  
Modern Psychology ◽  
Development Site ◽  
Approaches To Study ◽  
Methodological Approaches ◽  
Self Motion

У статті розглянуто сучасні підходи до інтерпретації категорії розвитку, розкрито теоретичні  та методологічні підходи до вивчення категорії розвитку у сучасній психології, визначено її психологічний  зміст,   моделі,   структуру   та   динаміку.   Категорія   розвитку   розглядається   як   епіцентр   наукової  проблематики у психології та як поняття інтегративного типу. Розвиток проаналізовано як категорію,  явище і проблему психології розвитку в різних аспектах аналізу. Розглянуто місце розвитку в системі  споріднених психологічних понять. У статті також аналізуються психологічні аспекти теоретичних та  методологічних  постнекласичних  тенденцій  вивчення  природи,  характеру  та  визначення  психічного  розвитку. Постнекласична парадигма та плюралістична методологія пізнання визначають розмитість  дисциплінарної мови  та  врахування  ролі  соціокультурного  контексту  при  вивченні  психологічних явищ.  Важливими тенденціями сучасного теоретико-методологічного стану психологічних досліджень розвитку  також є визнання неефективності моністичного підходу до його вивчення, взаємозв'язок теоретичних ідей  та   спроби   створення   метатеоретичних   схем,   постнекласичне   розуміння   розвитку   як   принципово  незавершеного   процесу   саморуху,   актуалізація   антропологічного   діапазону   проблем   та   посилення  спрямованості на роль культурного контексту в дослідженні розвитку людини.  The article deals with the modern approaches to the interpretation of the category of development, reveals  the theoretical and methodological approaches to study of development in modern psychology, its psychological  content, patterns, structure and dynamics. Category of development is viewed as an epicenter of scientific issues in  modern  psychology  and  the  concept  of  the  integrative  type.  Category  of  development  is  considered  as  the  phenomenon  and  the  problem  of  developmental  psychology  in  various  aspects  of  the  analysis.  Analyzed  the  development site in the related psychological concepts. The article analyzes the psychological aspects of theoretical  and methodological postnonclassical contemporary trends in the study of nature, character, and determination of  mental  development.  Postnonclassical  paradigm  and  pluralistic  methodology  of  knowledge  determine  the  disciplinary blurring and increase of the role of the analysis of socio-cultural context in the study of psychological  phenomenon. The important tendencies of modern theoretical and methodological state of psychological researches  of development are facts of inefficiency of the monistic approach to its study, interconnection of theoretical ideas  and   attempts   of  creating   metatheoretical   schemes,   postnonclassical   understanding   of   development   as   a  fundamentally  uncompleted  process  of  self-motion,  actualization  of  anthropological  range  of  problems  and  strengthening of focus on the role of cultural context in research of human development.   

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