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 <front>
  <journal-meta>
   <journal-id journal-id-type="publisher-id">Russian Journal of Biological Physics and Chemisrty</journal-id>
   <journal-title-group>
    <journal-title xml:lang="en">Russian Journal of Biological Physics and Chemisrty</journal-title>
    <trans-title-group xml:lang="ru">
     <trans-title>АКТУАЛЬНЫЕ ВОПРОСЫ БИОЛОГИЧЕСКОЙ ФИЗИКИ И ХИМИИ</trans-title>
    </trans-title-group>
   </journal-title-group>
   <issn publication-format="print">2499-9962</issn>
  </journal-meta>
  <article-meta>
   <article-id pub-id-type="publisher-id">54498</article-id>
   <article-categories>
    <subj-group subj-group-type="toc-heading" xml:lang="ru">
     <subject>Моделирование в биофизике</subject>
    </subj-group>
    <subj-group subj-group-type="toc-heading" xml:lang="en">
     <subject>Modelling in biophycis</subject>
    </subj-group>
    <subj-group>
     <subject>Моделирование в биофизике</subject>
    </subj-group>
   </article-categories>
   <title-group>
    <article-title xml:lang="en">Thermodynamic potentials of the ideal gas of nonlinear conformational perturbations - kinks activated in the ring plasmid pTTQ18</article-title>
    <trans-title-group xml:lang="ru">
     <trans-title>Термодинамические потенциалы идеального газа нелинейных конформационных возмущений - кинков, активированных в кольцевой плазмиде pTTQ18</trans-title>
    </trans-title-group>
   </title-group>
   <contrib-group content-type="authors">
    <contrib contrib-type="author">
     <name-alternatives>
      <name xml:lang="ru">
       <surname>Краснобаева</surname>
       <given-names>Л А</given-names>
      </name>
      <name xml:lang="en">
       <surname>Krasnobaeva</surname>
       <given-names>L A</given-names>
      </name>
     </name-alternatives>
     <email>kla1983@mail.ru</email>
     <xref ref-type="aff" rid="aff-1"/>
    </contrib>
    <contrib contrib-type="author">
     <name-alternatives>
      <name xml:lang="ru">
       <surname>Якушевич</surname>
       <given-names>Л. В.</given-names>
      </name>
      <name xml:lang="en">
       <surname>Yakushevich</surname>
       <given-names>L. V.</given-names>
      </name>
     </name-alternatives>
     <email>kind-@mail.ru</email>
     <xref ref-type="aff" rid="aff-2"/>
    </contrib>
   </contrib-group>
   <aff-alternatives id="aff-1">
    <aff>
     <institution xml:lang="ru">Сибирский государственный медицинский университет; Томский государственный университет</institution>
     <country>ru</country>
    </aff>
    <aff>
     <institution xml:lang="en">Siberian State Medical University; Tomsk State University</institution>
     <country>ru</country>
    </aff>
   </aff-alternatives>
   <aff-alternatives id="aff-2">
    <aff>
     <institution xml:lang="ru">ФИЦ «Пущинский научный центр биологических исследований РАН»</institution>
     <city>Пущино</city>
     <country>Россия</country>
    </aff>
    <aff>
     <institution xml:lang="en">PSCBR RAS</institution>
     <city>Pushchino</city>
     <country>Russian Federation</country>
    </aff>
   </aff-alternatives>
   <pub-date publication-format="print" date-type="pub" iso-8601-date="2020-03-25T20:22:29+03:00">
    <day>25</day>
    <month>03</month>
    <year>2020</year>
   </pub-date>
   <pub-date publication-format="electronic" date-type="pub" iso-8601-date="2020-03-25T20:22:29+03:00">
    <day>25</day>
    <month>03</month>
    <year>2020</year>
   </pub-date>
   <volume>5</volume>
   <issue>1</issue>
   <fpage>118</fpage>
   <lpage>124</lpage>
   <history>
    <date date-type="received" iso-8601-date="2020-03-20T20:22:29+03:00">
     <day>20</day>
     <month>03</month>
     <year>2020</year>
    </date>
    <date date-type="accepted" iso-8601-date="2020-03-20T20:22:29+03:00">
     <day>20</day>
     <month>03</month>
     <year>2020</year>
    </date>
   </history>
   <self-uri xlink:href="https://rusjbpc.ru/en/nauka/article/54498/view">https://rusjbpc.ru/en/nauka/article/54498/view</self-uri>
   <abstract xml:lang="ru">
    <p>Нелинейные конформационные возмущения - кинки, представляющие собой локально расплетенные участки двойной спирали ДНК, играют важную роль в процессах транскрипции, репликации, денатурации. В «нерелятивистском» приближении» кинки ДНК можно рассматривать как квазичастицы, обладающие определенной массой, скоростью и энергией покоя. Если в молекуле ДНК образовался не один, а N кинков, то правомерно поставить вопрос о статистике ансамбля из N кинков ДНК. Статистические свойства такого ансамбля до сих пор остаются малоизученными. В данной работе рассматривается вопрос о статистике ансамбля кинков, активированных в плазмиде pTTQ18. Для расчета термодинамических потенциалов применяется приближение идеального газа. Представлены аналитические формулы для статистической суммы, свободной энергии и энтропии в параметрах плазмиды pTTQ18. Построены графики температурной зависимости этих характеристик. Показано, что с ростом температуры свободная энергия ансамбля кинков уменьшается, а средняя энергия и энтропия увеличиваются, причем на одном и том же заданном интервале температур увеличение энтропии происходит довольно заметно, а увеличение средней энергии происходит очень медленно. Показано, что теплоемкость ансамбля кинков не зависит ни от температуры, ни от вида последовательности, а функция распределения кинков по скоростям имеет форму колокола, высота которого достигает максимума при нулевой скорости кинка.</p>
   </abstract>
   <trans-abstract xml:lang="en">
    <p>The nonlinear conformation distortions - kinks, which are locally unwound regions of the DNA double helix, play an important role in the processes of transcription, replication and denaturation. In the “nonrelativistic” approximation, the DNA kinks can be considered as quasiparticles with a certain mass, velocity, and rest energy. If not one, but N kinks are formed in the DNA molecule, then it is legitimate to raise the question of the statistics of an ensemble of N DNA kinks. The statistical properties of the ensemble are still poorly understood. In this paper, we consider the question of the statistics of an ensemble of kinks activated in the plasmid pTTQ18. The ideal gas approximation is used to calculate the thermodynamic potentials. Analytical formulas for the partition function, free energy, and entropy in the parameters of the plasmid are presented. The temperature dependence graphs of these characteristics are constructed. It is shown that with increasing temperature the free energy of the kink ensemble decreases, and the average energy and entropy increase, and in the same given temperature range, the increase in entropy is quite noticeable, and the average energy increases very slowly. The calculations show that the heat capacity of the kink ensemble does not depend either on temperature or on the type of sequence, and the kink velocity distribution function has the shape of a bell, the height of which reaches a maximum at zero kink velocity.</p>
   </trans-abstract>
   <kwd-group xml:lang="ru">
    <kwd>плазмида pTTQ18</kwd>
    <kwd>кинки ДНК</kwd>
    <kwd>статистика ансамбля кинков</kwd>
    <kwd>статистическая сумма</kwd>
    <kwd>свободная энергия</kwd>
    <kwd>энтропия</kwd>
   </kwd-group>
   <kwd-group xml:lang="en">
    <kwd>plasmid pTTQ18</kwd>
    <kwd>DNA kinks</kwd>
    <kwd>statistics of the ensemble of kinks</kwd>
    <kwd>statistical sum</kwd>
    <kwd>free energy</kwd>
    <kwd>entropy</kwd>
   </kwd-group>
  </article-meta>
 </front>
 <body>
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 </body>
 <back>
  <ref-list>
   <ref id="B1">
    <label>1.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Stark MJR. Multicopy expression vectors carrying the lac repressor gene for regulated high-level expression of genes in Escherichia coli. Gene, 1987, vol. 51, no. 2-3. pp. 255-67.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Stark MJR. Multicopy expression vectors carrying the lac repressor gene for regulated high-level expression of genes in Escherichia coli. Gene, 1987, vol. 51, no. 2-3. pp. 255-67.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B2">
    <label>2.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              The pTTQ18 DNA sequence [link]. URL: https://media.addgene.org/snapgene-media/v1.6.2-0-4b4ed87/sequences/18/42/121842/addgene-plasmid-69122-sequence-121842.gbk
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              The pTTQ18 DNA sequence [link]. URL: https://media.addgene.org/snapgene-media/v1.6.2-0-4b4ed87/sequences/18/42/121842/addgene-plasmid-69122-sequence-121842.gbk
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B3">
    <label>3.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Grinevich A.A., Ryasik A.A., Yakushevich L.V. Trajectories of DNA bubles. Chaos, Solitons &amp; Fractals, 2015, vol. 75, pp. 62-75. DOI: 10.1016/j.chaos.2015.02.009.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Grinevich A.A., Ryasik A.A., Yakushevich L.V. Trajectories of DNA bubles. Chaos, Solitons &amp; Fractals, 2015, vol. 75, pp. 62-75. DOI: 10.1016/j.chaos.2015.02.009.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B4">
    <label>4.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Якушевич Л.В., Балашова В.Н., Закирьянов Ф.К. О движении кинка ДНК под действием постоянного торсионного момента. Математическая биология и биоинформатика, 2016, т. 11, № 1, c. 81-90, DOI: 10.17537/2016.11.81. @@[Yakushevich L.V., Balashova V.N., Zakiryanov F.K. On the DNA kink motion under the action of constant torque. Mathematical biology and bioinformatics, 2016, vol. 11, no.1, pp. 81-90, DOI:10.17537/2016.11.81. (In Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Yakushevich L.V., Balashova V.N., Zakir'yanov F.K. O dvizhenii kinka DNK pod deystviem postoyannogo torsionnogo momenta. Matematicheskaya biologiya i bioinformatika, 2016, t. 11, № 1, c. 81-90, DOI: 10.17537/2016.11.81. @@[Yakushevich L.V., Balashova V.N., Zakiryanov F.K. On the DNA kink motion under the action of constant torque. Mathematical biology and bioinformatics, 2016, vol. 11, no.1, pp. 81-90, DOI:10.17537/2016.11.81. (In Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B5">
    <label>5.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Shikhovtseva E.S., Nazarov V.N. Non-linear longitudinal compression effect on dynamics of the transcription bubble in DNA. Biophysical Chemistry, 2016, vol. 214-215, pp. 47-53. DOI: 10.1016/j.bpc.2016.05.005.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Shikhovtseva E.S., Nazarov V.N. Non-linear longitudinal compression effect on dynamics of the transcription bubble in DNA. Biophysical Chemistry, 2016, vol. 214-215, pp. 47-53. DOI: 10.1016/j.bpc.2016.05.005.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B6">
    <label>6.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Grinevich A.A., Ryasik A.A., Yakushevich L.V. Modeling the DNA bubbles dynamics. Journal of Biomolecular Structure and Dynamics, 2015, vol. 33, p. 84. DOI: 10.1080/07391102.2015.1032763.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Grinevich A.A., Ryasik A.A., Yakushevich L.V. Modeling the DNA bubbles dynamics. Journal of Biomolecular Structure and Dynamics, 2015, vol. 33, p. 84. DOI: 10.1080/07391102.2015.1032763.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B7">
    <label>7.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Grinevich A.A., Yakushevich L.V. The inﬂuence of the DNA torque on the dynamics of transcription bubbles in plasmid pTTQ18. J. Theor. Biol., 2018, vol. 453, pp. 68-77. DOI: 10.1016/j.jtbi.2018.04.036.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Grinevich A.A., Yakushevich L.V. The inﬂuence of the DNA torque on the dynamics of transcription bubbles in plasmid pTTQ18. J. Theor. Biol., 2018, vol. 453, pp. 68-77. DOI: 10.1016/j.jtbi.2018.04.036.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B8">
    <label>8.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Forth S., Sheinin M.Y., Inman J. et al. Torque measurement at the single-molecule level. Annu Rev Biophys., 2013, vol. 42, no. 1, p. 583-604. DOI: 10.1146/annurev-biophys-083012-130412.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Forth S., Sheinin M.Y., Inman J. et al. Torque measurement at the single-molecule level. Annu Rev Biophys., 2013, vol. 42, no. 1, p. 583-604. DOI: 10.1146/annurev-biophys-083012-130412.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B9">
    <label>9.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Severin E.S. Biochemistry. Moscow: GEOTAR-Media, 2016, 750 p.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Severin E.S. Biochemistry. Moscow: GEOTAR-Media, 2016, 750 p.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B10">
    <label>10.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Yakushevich L.V., Krasnobaeva L.A. Ensemble of DNA Kinks. EPJ Web of Conferences, 2019, vol. 224, p. 03005. DOI: 10.1051/epjconf/201922403005.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Yakushevich L.V., Krasnobaeva L.A. Ensemble of DNA Kinks. EPJ Web of Conferences, 2019, vol. 224, p. 03005. DOI: 10.1051/epjconf/201922403005.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B11">
    <label>11.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Краснобаева Л.А., Якушевич Л.В. Динамические и статистические свойства кинков ДНК. Биофизика, 2020, т. 65, № 1, c. 29-35. DOI: 10.1134/S0006350920010091. @@[Krasnobaeva L.A., Yakushevich L.V. The Dynamic and Statistical Properties of DNA Kinks. Biophysics, 2020, vol. 65, no. 1, pp. 29-35. DOI: 10.1134/S0006350920010091. (In Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Krasnobaeva L.A., Yakushevich L.V. Dinamicheskie i statisticheskie svoystva kinkov DNK. Biofizika, 2020, t. 65, № 1, c. 29-35. DOI: 10.1134/S0006350920010091. @@[Krasnobaeva L.A., Yakushevich L.V. The Dynamic and Statistical Properties of DNA Kinks. Biophysics, 2020, vol. 65, no. 1, pp. 29-35. DOI: 10.1134/S0006350920010091. (In Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B12">
    <label>12.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Yakushevich L.V., Krasnobaeva L.A. A new approach to studies of nonlinear dynamics of kinks activated in inhomogeneous polynucleotide chains. Int. J. Nonl. Mech., 2008, vol. 43, pp. 1074-1081. DOI: 10.1016/j.ijnonlinmec. 2008.05.00.b0100.
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Yakushevich L.V., Krasnobaeva L.A. A new approach to studies of nonlinear dynamics of kinks activated in inhomogeneous polynucleotide chains. Int. J. Nonl. Mech., 2008, vol. 43, pp. 1074-1081. DOI: 10.1016/j.ijnonlinmec. 2008.05.00.b0100.
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B13">
    <label>13.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Караваев Г.Ф. Основные принципы статистической физики. Томск: ТГУ, 1993, 75 c. @@[Karavaev G.F. Basic Principles of Statistical Physics. Tomsk: TSU, 1993, 75 p. (In Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Karavaev G.F. Osnovnye principy statisticheskoy fiziki. Tomsk: TGU, 1993, 75 c. @@[Karavaev G.F. Basic Principles of Statistical Physics. Tomsk: TSU, 1993, 75 p. (In Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B14">
    <label>14.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Квасников И.А. Термодинамика и статистическая физика. Москва: Эдиториал УРСС, 2010, 448 c. @@[Kvasnikov I.A. Thermodynamics and Statistical Physics. Moscow: Editorial URSS, 2010, 448 p. (In Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Kvasnikov I.A. Termodinamika i statisticheskaya fizika. Moskva: Editorial URSS, 2010, 448 c. @@[Kvasnikov I.A. Thermodynamics and Statistical Physics. Moscow: Editorial URSS, 2010, 448 p. (In Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B15">
    <label>15.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Базаров И.П. Термодинамика. Москва: Высшая школа, 1991, 376 с. [Bazarov I.P. Thermodynamics. Moscow: Higher School, 1991, 376 p. (in Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Bazarov I.P. Termodinamika. Moskva: Vysshaya shkola, 1991, 376 s. [Bazarov I.P. Thermodynamics. Moscow: Higher School, 1991, 376 p. (in Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B16">
    <label>16.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Леванов А.В., Антипенко Э.Е. Определение термодинамических свойств статистическими методами. Классический идеальный газ. Москва: МГУ, 2006, 44 с. @@[Levanov A.V., Antipenko E.E. Determination of thermodynamic properties by statistical methods. Classic perfect gas. Moscow: MSU, 2006, 44 p. (in Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Levanov A.V., Antipenko E.E. Opredelenie termodinamicheskih svoystv statisticheskimi metodami. Klassicheskiy ideal'nyy gaz. Moskva: MGU, 2006, 44 s. @@[Levanov A.V., Antipenko E.E. Determination of thermodynamic properties by statistical methods. Classic perfect gas. Moscow: MSU, 2006, 44 p. (in Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
   <ref id="B17">
    <label>17.</label>
    <citation-alternatives>
     <mixed-citation xml:lang="ru">
            
              Зоммерфельд А. Термодинамика и статистическая физика. Москва, 1955, 482 c. @@[Sommerfeld A. Thermodynamics and Statistical Physics. Moscow, 1955, 482 p. (in Russ.)]
            
          </mixed-citation>
     <mixed-citation xml:lang="en">
            
              Zommerfel'd A. Termodinamika i statisticheskaya fizika. Moskva, 1955, 482 c. @@[Sommerfeld A. Thermodynamics and Statistical Physics. Moscow, 1955, 482 p. (in Russ.)]
            
          </mixed-citation>
    </citation-alternatives>
   </ref>
  </ref-list>
 </back>
</article>
