{"title":"A/T tracts domination problem in the human genome","authors":"V. M. Komarov, A. Samchenko, M. Kondratiev","doi":"10.17537/ICMBB18.114","DOIUrl":"https://doi.org/10.17537/ICMBB18.114","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123485993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mathematical modelling of the ryanodine receptor’s activation time dependence on magnesium","authors":"B. Iaparov, V. V. Ivchenko","doi":"10.17537/ICMBB18.69","DOIUrl":"https://doi.org/10.17537/ICMBB18.69","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125199307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Kuzin, R. A. Kuzin, S. Timerbulatov, S. A. Ulemaeva, A. G. Khakimov
{"title":"Instability Interactions of Blood Vessel","authors":"A. Kuzin, R. A. Kuzin, S. Timerbulatov, S. A. Ulemaeva, A. G. Khakimov","doi":"10.17537/ICMBB18.16","DOIUrl":"https://doi.org/10.17537/ICMBB18.16","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130540430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Theoretical analysis of the mechanism of microtubule rescue due to embedded GTP islands","authors":"А. Zaitsev, V. Mustyatsa, N. Gudimchuk","doi":"10.17537/ICMBB18.37","DOIUrl":"https://doi.org/10.17537/ICMBB18.37","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126580573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The study of metagenomes of oceanic microbiota","authors":"A. A. Zimin, N. Nazipova","doi":"10.17537/ICMBB18.105","DOIUrl":"https://doi.org/10.17537/ICMBB18.105","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126623820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K. Romanenkov, G. Tyulbasheva, M. Ustinin, N. Nazipova
{"title":"Creation of a web server for de novo genome assembly on the basis of combining the results obtained by various assemblers","authors":"K. Romanenkov, G. Tyulbasheva, M. Ustinin, N. Nazipova","doi":"10.17537/ICMBB18.104","DOIUrl":"https://doi.org/10.17537/ICMBB18.104","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129157562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
K. Ushenin, A. Dokuchaev, S. Magomedova, O. Sopov, V. Kalinin, O. Solovyova
{"title":"Models of human heart and torso electrophysiology verified against clinical data","authors":"K. Ushenin, A. Dokuchaev, S. Magomedova, O. Sopov, V. Kalinin, O. Solovyova","doi":"10.17537/ICMBB18.41","DOIUrl":"https://doi.org/10.17537/ICMBB18.41","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"2 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"113938618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Klimenko, Z. S. Mustafin, S. Lashin, Y. Matushkin
{"title":"Simulation of the evolution of metabolism amplification and reduction in prokaryotes inhabiting spatially heterogeneous environments","authors":"A. Klimenko, Z. S. Mustafin, S. Lashin, Y. Matushkin","doi":"10.17537/ICMBB18.15","DOIUrl":"https://doi.org/10.17537/ICMBB18.15","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116834671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. I. Pyatkov, A. Zaytsev, M. Olshevets, N. S. Fialko
Процессы переноса заряда в ДНК моделируются с помощью вычислительного эксперимента. Мы рассматриваем модель, основанную на гамильтониане Холстейна в полуклассическом приближении, для учета температуры используется ланжевеновский термостат. Характерные времена квантовой и классической подсистем для модели ДНК сильно различны, на два порядка и больше. Ранее было показано, что термодинамические величины – полная энергия системы, электронная часть теплоемкости и т.п. – в термодинамически равновесном состоянии зависят не от значений коэффициентов модели, а от их соотношений. Поэтому сами величины можно рассчитывать, используя «ускоряющие» значения параметров, при которых система приходит к равновесному состоянию за сравнительно небольшое время. Ситуация меняется, если нас интересует динамика заряда в ДНК из начального состояния «заряд локализован на сайте-доноре» до термодинамического равновесия. В этом случае расчетное время может быть очень большим, и появляется вопрос о корректности моделирования. Этот вопрос мы исследовали с помощью тестовых расчетов. Проверено два метода интегрирования с искусственной нормировкой. Расчетные параметры соответствуют гуаниновым и адениновым сайтам. По результатам тестов выбран оптимальный метод для выполнения серийных расчетов и определен максимальный шаг интегрирования при значениях параметров, характерных для гетерогенных фрагментов ДНК.
{"title":"On the optimal integration step in the numerical experiments on the charge dynamics in heterogeneous DNA","authors":"M. I. Pyatkov, A. Zaytsev, M. Olshevets, N. S. Fialko","doi":"10.17537/ICMBB18.65","DOIUrl":"https://doi.org/10.17537/ICMBB18.65","url":null,"abstract":"Процессы переноса заряда в ДНК моделируются с помощью вычислительного эксперимента. Мы рассматриваем модель, основанную на гамильтониане Холстейна в полуклассическом приближении, для учета температуры используется ланжевеновский термостат. Характерные времена квантовой и классической подсистем для модели ДНК сильно различны, на два порядка и больше. Ранее было показано, что термодинамические величины – полная энергия системы, электронная часть теплоемкости и т.п. – в термодинамически равновесном состоянии зависят не от значений коэффициентов модели, а от их соотношений. Поэтому сами величины можно рассчитывать, используя «ускоряющие» значения параметров, при которых система приходит к равновесному состоянию за сравнительно небольшое время. Ситуация меняется, если нас интересует динамика заряда в ДНК из начального состояния «заряд локализован на сайте-доноре» до термодинамического равновесия. В этом случае расчетное время может быть очень большим, и появляется вопрос о корректности моделирования. Этот вопрос мы исследовали с помощью тестовых расчетов. Проверено два метода интегрирования с искусственной нормировкой. Расчетные параметры соответствуют гуаниновым и адениновым сайтам. По результатам тестов выбран оптимальный метод для выполнения серийных расчетов и определен максимальный шаг интегрирования при значениях параметров, характерных для гетерогенных фрагментов ДНК.","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"109 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127079034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
V. Bystrov, E. Paramonova, L. Avakyan, J. Coutinho, A. Bystrova
{"title":"Defects in Hydroxyapatite: structure and properties, calculations from the first principles","authors":"V. Bystrov, E. Paramonova, L. Avakyan, J. Coutinho, A. Bystrova","doi":"10.17537/ICMBB18.1","DOIUrl":"https://doi.org/10.17537/ICMBB18.1","url":null,"abstract":"","PeriodicalId":168323,"journal":{"name":"Proceedings of the International Conference \"Mathematical Biology and Bioinformatics\"","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128179889","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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