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A Mathematical Model for Vibration Behavior Analysis of DNA and Using a Resonant Frequency of DNA for Genome Engineering

Abstract

The DNA molecule is the most evolved and most complex molecule created by nature. The primary role of DNA in medicine is long-term storage of genetic information. Genetic modifying is one of the most critical challenges that scientists face. On the other hand, it is said that under the influence of acoustic, electromagnetic, and scalar waves, the genetic code of DNA can be read or rewritten. In this article, the most accurate and comprehensive dynamic model will be presented for DNA. Each of the two strands is modeled with an out of plane curved beam and then by doubling this two strands with springs, consider the hydrogen bond strength between this two strands. Beams are traditionally descriptions of mechanical engineering structural elements or building. However, any structure such as automotive automobile frames, aircraft components, machine frames, and other mechanical or structural systems contain beam structures that are designed to carry lateral loads are analyzed similarly. Also, in this model, the mass of the nucleobases in the DNA structure, the effects of the fluid surrounding the DNA (nucleoplasm) and the effects of temperature changes are also considered. Finally, by deriving governing equations from Hamilton’s principle method and solving these equations with the generalized differential quadrature method (GDQM), the frequency and mode shape of the DNA is obtained for the first time. In the end, validation of the obtained results from solving the governing equations of mathematical model compared to the obtained results from the COMSOL software is confirmed. By the help of these results, a conceptual idea for controlling cancer with using the DNA resonance frequency is presented. This idea will be presented to stop the cancerous cell’s protein synthesis and modifying DNA sequence and genetic manipulation of the cell. On the other hand, by the presented DNA model and by obtaining DNA frequency, experimental studies of the effects of waves on DNA such as phantom effect or DNA teleportation can also be studied scientifically and precisely.

Introduction

Deoxyribonucleic acid, more commonly known as DNA, is an evolved molecule that contains the genetic code of organisms. Every living thing has DNA within their cells. It is important for inheritance, coding for proteins and the genetic instruction guide for life and its processes. DNA holds the instructions for an organism or each cell development processes, reproduction and ultimately death. Over the past decades, empirical discussions have been proposed to modify the genes in the DNA. These changes have been much discussed in the medical field by drawing on applications such as treatment, preventing the development of cancer, or erupting an organ (for example, a tooth). On the other hand, it should be noted that only 3% of DNA capacity is considered in medical fields. In the last two decades, a topic called “wave genome” has been raised by Russian scientists, which states that 97% of other DNA is not only inapplicable but also has a more significant role; because DNA can be affected by acoustic, electromagnetic, and scalar waves. Under the influence of these waves, the genetic code can be read or rewritten. Another claim of Russian scientists is that DNA is a biological network that binds all humans. About impressionability of DNA from the wave frequency, many experimental research studies have been carried out which have opened a new branch in science, called wave genome. Konstantin Meyl adapted the scalar waves described by Nicola Tesla to biology and proposed the relationship between the scalar waves and DNA1. Greg Braddon and colleagues in 3 experiments investigated the impressionability of DNA from human emotions2. Rein and Mccraty studied the impact of music on the DNA3,4,5. Another study was carried out on the effect of sound waves on the synthesis and genes of chrysanthemum6. Peter Garjajev and his research group proved that DNA can be reprogrammed by words and using the correct resonant frequencies of DNA7,8. Russian quantum biologist Poponin tried to prove that human DNA has a direct effect on the physical world using some experiments9. Also, he found out that our DNA can cause disturbing patterns in the vacuum, thus producing magnetized microscopic wormholes10. Nobel Prize-winning scientist Luc Montagnier known for his study on HIV and AIDS, claims to have demonstrated that DNA can be generated by teleportation through quantum imprint and also showed that DNA emits electromagnetic signals that teleport the DNA to other places, such as water molecules11,12.

About Mathematical Modeling of DNA, three eminent mathematical models have been proposed for describing DNA. The most famous model presented is the PBD (Peyrard-Bishop-Dauxois) model13, although this model has been updated by various researchers14,15,16,17,18, the models presented in these studies usually have at least three significant weaknesses such as being discrete, not being outside the plane, not being spiral, and not considering the position of nucleobases. Examples of the PBD model are displayed in Fig. 1. The other model is a rod model looking at DNA on a larger scale19,20,21, with significant weaknesses, including the lack of attention to the nucleobase positions and the hydrogen bond, as well as considering DNA with one strand (Fig. 2). There is another model called SIDD (stress-induced DNA duplex destabilization) that is entirely mathematical and applied in the field of molecular dynamics22,23. These models mentioned were mostly designed to investigate the vibration of DNA, and there are several models available in other fields such as DNA’s entropic elasticity24 and bending of a DNA25,26. A beam is a structural element that primarily resists loads applied laterally to the beam axis. Its mode of deflection is primarily by bending. The Timoshenko beam theory takes the shear deformation and rotational bending effects into consideration for describing the behavior of thick beams. On the other hand, all previous studies related to curved beam vibrations focus on out of plane vibration of curved beams (with inline coordinates) and do not study out of plane vibration of the curved beams. A.Y.T. Leung is the only reference derived from the governing equations for a helical beam with rectangular cross-sections with pre-twist27.

According to the above contents based on the necessity of DNA vibration analysis and the weaknesses of the previously proposed models, the necessity of carrying out this research becomes more evident. The dynamic model presented for DNA here has been named GMDM (Ghadiri Marvi DNA Model), it is provided by connecting two out of plane nano curved beams with spring and a damper. Each of the beams is a model for one of the two DNA strands (sugar-phosphate backbone). Also, spring and damper is a model for hydrogen bonds between nitrogen-containing nucleobases. The effects of the nucleobases (cytosine, guanine, adenine, and thymine) are also considered with their mass (Fig. 3). Also, the effects of DNA surrounding fluid (nucleoplasm) have been applied by using the Navier Stokes equations. Effects of temperature change on DNA are also applied to equations with external work. Finally, by using the relations of all the effects that mentioned above and using the Hamilton principle, the DNA equations will be extracted.

It should be noted that with the help of the theory of nonlocal, the effects of size were considered. By solving these equations, DNA natural frequency will be obtained for the first time. Numerical method can solve the equations derived from Hamilton’s principle method. The generalized differential quadrature method (GDQM) is one of the most numerical methods can be used for solving governing differential equations.

The idea brought up in this study is that if DNA is influenced by wave frequencies as much as DNA natural frequency then resonance occurs and DNA vibrates with large amplitude oscillations. With many shakes, DNA strands go up and down and at this moment a nucleobase in the nucleotide of one of the DNA strands establishes a hydrogen bond with the nucleobases lower or upper and the nucleobase aligns itself on the other DNA strands. This mechanism and idea which is presented schematically in Fig. 4, can cause disorganization in a sequence of DNA, and finally, with the help of a restriction enzyme (endonuclease), DNA in the cancerous cell loss of the ability to biosynthesis of proteins and the cancer is controlled just like the CRISPR/CAS9 technology.

Nonlocal Elasticity Theory

In accordance with the nonlocal elasticity theory, the stress state at a reference point in an elastic continuum depends not only on the strain components at the same position but also a function of strains of all points in the neighbor regions. Therefore, the nonlocal stress tensor’s at point x is expressed as:

σ(x)T(x)==VK(|xx|,τ)T(x)dv(x)C(x):ε(x)σ(x)=∫VK(|x′−x|,τ)T(x′)dv(x′)T(x)=C(x):ε(x)
(1)

where T(x) is the classical, macroscopic stress tensor at point x related to strain by Hooke’s law with Eq. (1). C(x) is the fourth-order elasticity tensor, ε(x) is the strain tensor and K(|x′ − x|, τ) denotes nonlocal modulus. |x′ − x| represents the distance and τ is a material constant that depends on the internal and external characteristic length defined as τ=e0aLτ=e0aL where e0 is a constant appropriate to each material, a is an internal characteristics length (e.g., bonds length) and L is an external characteristics length (e.g., wavelength).

Solving the integral constitutive relation in Eq. (1) is difficult. Thus, equivalent relation in a differential form was proposed by Eringen28,29 as follows:

T=(1τ2L22)σ,τ=e0aLT=(1−τ2L2∇2)σ,τ=e0aL
(2)

2 is the Laplacian operator

Beam theory and displacement of a double helical nanobeam

An out of plane curved beam is the beam having a twist and curvature around its central axis. The geometry situation of this model needs to choose the coordinate system that every moment changes its vector location (Fig. 5). Thus, for the analysis of the out of plane curved beam, Frenet triad must be used.

A Mathematical Model for Vibration Behavior Analysis of DNA and Using a Resonant Frequency of DNA for Genome Engineering

Abstract

The DNA molecule is the most evolved and most complex molecule created by nature. The primary role of DNA in medicine is long-term storage of genetic information. Genetic modifying is one of the most critical challenges that scientists face. On the other hand, it is said that under the influence of acoustic, electromagnetic, and scalar waves, the genetic code of DNA can be read or rewritten. In this article, the most accurate and comprehensive dynamic model will be presented for DNA. Each of the two strands is modeled with an out of plane curved beam and then by doubling this two strands with springs, consider the hydrogen bond strength between this two strands. Beams are traditionally descriptions of mechanical engineering structural elements or building. However, any structure such as automotive automobile frames, aircraft components, machine frames, and other mechanical or structural systems contain beam structures that are designed to carry lateral loads are analyzed similarly. Also, in this model, the mass of the nucleobases in the DNA structure, the effects of the fluid surrounding the DNA (nucleoplasm) and the effects of temperature changes are also considered. Finally, by deriving governing equations from Hamilton’s principle method and solving these equations with the generalized differential quadrature method (GDQM), the frequency and mode shape of the DNA is obtained for the first time. In the end, validation of the obtained results from solving the governing equations of mathematical model compared to the obtained results from the COMSOL software is confirmed. By the help of these results, a conceptual idea for controlling cancer with using the DNA resonance frequency is presented. This idea will be presented to stop the cancerous cell’s protein synthesis and modifying DNA sequence and genetic manipulation of the cell. On the other hand, by the presented DNA model and by obtaining DNA frequency, experimental studies of the effects of waves on DNA such as phantom effect or DNA teleportation can also be studied scientifically and precisely.

Introduction

Deoxyribonucleic acid, more commonly known as DNA, is an evolved molecule that contains the genetic code of organisms. Every living thing has DNA within their cells. It is important for inheritance, coding for proteins and the genetic instruction guide for life and its processes. DNA holds the instructions for an organism or each cell development processes, reproduction and ultimately death. Over the past decades, empirical discussions have been proposed to modify the genes in the DNA. These changes have been much discussed in the medical field by drawing on applications such as treatment, preventing the development of cancer, or erupting an organ (for example, a tooth). On the other hand, it should be noted that only 3% of DNA capacity is considered in medical fields. In the last two decades, a topic called “wave genome” has been raised by Russian scientists, which states that 97% of other DNA is not only inapplicable but also has a more significant role; because DNA can be affected by acoustic, electromagnetic, and scalar waves. Under the influence of these waves, the genetic code can be read or rewritten. Another claim of Russian scientists is that DNA is a biological network that binds all humans. About impressionability of DNA from the wave frequency, many experimental research studies have been carried out which have opened a new branch in science, called wave genome. Konstantin Meyl adapted the scalar waves described by Nicola Tesla to biology and proposed the relationship between the scalar waves and DNA1. Greg Braddon and colleagues in 3 experiments investigated the impressionability of DNA from human emotions2. Rein and Mccraty studied the impact of music on the DNA3,4,5. Another study was carried out on the effect of sound waves on the synthesis and genes of chrysanthemum6. Peter Garjajev and his research group proved that DNA can be reprogrammed by words and using the correct resonant frequencies of DNA7,8. Russian quantum biologist Poponin tried to prove that human DNA has a direct effect on the physical world using some experiments9. Also, he found out that our DNA can cause disturbing patterns in the vacuum, thus producing magnetized microscopic wormholes10. Nobel Prize-winning scientist Luc Montagnier known for his study on HIV and AIDS, claims to have demonstrated that DNA can be generated by teleportation through quantum imprint and also showed that DNA emits electromagnetic signals that teleport the DNA to other places, such as water molecules11,12.

About Mathematical Modeling of DNA, three eminent mathematical models have been proposed for describing DNA. The most famous model presented is the PBD (Peyrard-Bishop-Dauxois) model13, although this model has been updated by various researchers14,15,16,17,18, the models presented in these studies usually have at least three significant weaknesses such as being discrete, not being outside the plane, not being spiral, and not considering the position of nucleobases. Examples of the PBD model are displayed in Fig. 1. The other model is a rod model looking at DNA on a larger scale19,20,21, with significant weaknesses, including the lack of attention to the nucleobase positions and the hydrogen bond, as well as considering DNA with one strand (Fig. 2). There is another model called SIDD (stress-induced DNA duplex destabilization) that is entirely mathematical and applied in the field of molecular dynamics22,23. These models mentioned were mostly designed to investigate the vibration of DNA, and there are several models available in other fields such as DNA’s entropic elasticity24 and bending of a DNA25,26. A beam is a structural element that primarily resists loads applied laterally to the beam axis. Its mode of deflection is primarily by bending. The Timoshenko beam theory takes the shear deformation and rotational bending effects into consideration for describing the behavior of thick beams. On the other hand, all previous studies related to curved beam vibrations focus on out of plane vibration of curved beams (with inline coordinates) and do not study out of plane vibration of the curved beams. A.Y.T. Leung is the only reference derived from the governing equations for a helical beam with rectangular cross-sections with pre-twist27.

Figure 1
figure1

Schematic of PBD model (a) and its updates (b–d). These images have been drawn with Adobe Photoshop CC 2018.

Figure 2
figure2

A rod model that looks at DNA on a larger scale. This image has been designed with Adobe Photoshop CC 2018.

According to the above contents based on the necessity of DNA vibration analysis and the weaknesses of the previously proposed models, the necessity of carrying out this research becomes more evident. The dynamic model presented for DNA here has been named GMDM (Ghadiri Marvi DNA Model), it is provided by connecting two out of plane nano curved beams with spring and a damper. Each of the beams is a model for one of the two DNA strands (sugar-phosphate backbone). Also, spring and damper is a model for hydrogen bonds between nitrogen-containing nucleobases. The effects of the nucleobases (cytosine, guanine, adenine, and thymine) are also considered with their mass (Fig. 3). Also, the effects of DNA surrounding fluid (nucleoplasm) have been applied by using the Navier Stokes equations. Effects of temperature change on DNA are also applied to equations with external work. Finally, by using the relations of all the effects that mentioned above and using the Hamilton principle, the DNA equations will be extracted.

Figure 3
figure3

(a) Imagined shape for DNA43 © 2013 Nature Education Adapted from Pray, L. (2008) Discovery of DNA structure and function: Watson and Crick. Nature Education 1(1):100. All rights reserved. (b) The GMDM Mathematical model, which is presented in this paper for dynamics investigations of DNA. This image has been modeled with COMSOL Multiphysics 5.3a and edited with Adobe Photoshop CC 2018.

It should be noted that with the help of the theory of nonlocal, the effects of size were considered. By solving these equations, DNA natural frequency will be obtained for the first time. Numerical method can solve the equations derived from Hamilton’s principle method. The generalized differential quadrature method (GDQM) is one of the most numerical methods can be used for solving governing differential equations.

The idea brought up in this study is that if DNA is influenced by wave frequencies as much as DNA natural frequency then resonance occurs and DNA vibrates with large amplitude oscillations. With many shakes, DNA strands go up and down and at this moment a nucleobase in the nucleotide of one of the DNA strands establishes a hydrogen bond with the nucleobases lower or upper and the nucleobase aligns itself on the other DNA strands. This mechanism and idea which is presented schematically in Fig. 4, can cause disorganization in a sequence of DNA, and finally, with the help of a restriction enzyme (endonuclease), DNA in the cancerous cell loss of the ability to biosynthesis of proteins and the cancer is controlled just like the CRISPR/CAS9 technology.

Figure 4
figure4

(a) DNA’s shape before reaching resonant frequency. (b) DNA’s shape after reaching resonant frequency. (c) Establishes a hydrogen bond between the nucleobases upper with nucleobases lower. (d) Removal of additional and remaining nucleotides with the help of restriction enzyme. (e) New DNA’s shape and disorganization in a sequence of DNA. These images have been modeled with COMSOL Multiphysics 5.3a and edited with Adobe Photoshop CC 2018.

Nonlocal Elasticity Theory

In accordance with the nonlocal elasticity theory, the stress state at a reference point in an elastic continuum depends not only on the strain components at the same position but also a function of strains of all points in the neighbor regions. Therefore, the nonlocal stress tensor’s at point x is expressed as:

σ(x)T(x)==VK(|xx|,τ)T(x)dv(x)C(x):ε(x)σ(x)=∫VK(|x′−x|,τ)T(x′)dv(x′)T(x)=C(x):ε(x)
(1)

where T(x) is the classical, macroscopic stress tensor at point x related to strain by Hooke’s law with Eq. (1). C(x) is the fourth-order elasticity tensor, ε(x) is the strain tensor and K(|x′ − x|, τ) denotes nonlocal modulus. |x′ − x| represents the distance and τ is a material constant that depends on the internal and external characteristic length defined as τ=e0aLτ=e0aL where e0 is a constant appropriate to each material, a is an internal characteristics length (e.g., bonds length) and L is an external characteristics length (e.g., wavelength).

Solving the integral constitutive relation in Eq. (1) is difficult. Thus, equivalent relation in a differential form was proposed by Eringen28,29 as follows:

T=(1τ2L22)σ,τ=e0aLT=(1−τ2L2∇2)σ,τ=e0aL
(2)

2 is the Laplacian operator

Beam theory and displacement of a double helical nanobeam

An out of plane curved beam is the beam having a twist and curvature around its central axis. The geometry situation of this model needs to choose the coordinate system that every moment changes its vector location (Fig. 5). Thus, for the analysis of the out of plane curved beam, Frenet triad must be used.

Figure 5

An out of plane curved beam. This image has been modeled with CATIA V5 and edited with Adobe Photoshop CC 2018.

The base beam theory used to model an out of plane curved beam is Timoshenko beam theory. By following Timoshenko’s assumption, the displacements u are defined as consisting of two parts, part one is the displacements at the centerline along the local axes v and part 2 is the rotations of the cross-section θ. This two parts according to Timoshenko’s assumption, only defined at the x3 axis.

u={u1(x1,x2,x3)u2(x1,x2,x3)u3(x1,x2,x3)}={ν1(x3)ν2(x3)ν3(x3)}+[00x200x1x2x10]{θ1(x3)θ2(x3)θ3(x3)}=[10001000100x200x1x2x10]R=NR,R=[ν1ν2ν3θ1θ2θ3]eiωt=reiωtu={u1(x1,x2,x3)u2(x1,x2,x3)u3(x1,x2,x3)}={ν1(x3)ν2(x3)ν3(x3)}+[00−x200x1x2−x10]{θ1(x3)θ2(x3)θ3(x3)}=[10000−x201000x1001x2−x10]R=NR,R=[ν1ν2ν3θ1θ2θ3]eiωt=reiωt
(3)

In Eq. (3r is the vector of the main displacement functions.

In Fig. 6, a small cut of a cross section of a beam has been displayed.

To find the strain vector of out of plane curved beams must be differentiated the displacement concerning the arc length x3.

With using the Frenet triad and its special differential can be derived the displacement vector gradient of an out of plane curved beam as follows27:

{u,1u,2u,3}={ux1ux2ux3}=[0000000(τμ)Cκ000000τμ0Sκ000000CκSκ0000001Cκx2Sκx20001000Cκx1Sκx10010100x1(τμ)x2(τμ)κ(Cx2+Sx1)00000010000000001000000000100000000x200000000x1000000x2x10]{RR}{u,1u,2u,3}={∂u∂x1∂u∂x2∂u∂x3}=[0000000000000000010000000000−1000000000000−10000000000000000000001000000000τ−μ−Cκ−Cκx2Cκx1x1(τ−μ)10000−x2−(τ−μ)0SκSκx2−Sκx1x2(τ−μ)01000x1Cκ−Sκ000−κ(Cx2+Sx1)001×2−x10]{RR′}
(4)

Parameters τ,κ,μτ,κ,μ used in the matrix Eq. (4) respectively represent tortuosity, curvature and pre-twist rate, in which, C=cos(μs)C=cos⁡(μs)S=sin(μs)S=sin⁡(μs) and μsμs is twist per length.

The non-vanishing strain matrix based on the Timoshenko’s assumption are derived as:

ε=[0τμCκτμ0SκCκSκ0Cκx2Sκx2+10Cκx11Sκx10x1(τμ)x2(τμ)κ(Cx2+Sx1)10001000100x200x1x2x10]{RR}ε=[0τ−μ−Cκ−Cκx2Cκx−1−1×1(τ−μ)10000−x2−τ−μ0SκSκx2+1−Sκx1x2(τ−μ)01000x1Cκ−Sκ000−κ(Cx2+Sx1)001−x2−x10]{RR′}
(5)

For simplicity in the use of nonlocal theory, strain matrix is separated into three matrices:

ε=(e0+x1e1+x2e2){RR}ε=(e0+x1e1+x2e2){RR′}
(6)

In which:

e0=[0(τμ)Cκτμ0SκCκSκ0010100000100010001000000000]e1=[000000000000CκSκ0(τμ)0κS000000000000001010]e2=[000000000CκSκ00000(τμ)κC000000000001000100]e0=[0τ−μ−Cκ0−10100000−(τ−μ)0Sκ100010000Cκ−Sκ0000001000]e1=[0000Cκ(τ−μ)0000000000−Sκ000000100000−κS0000−10]e2=[000−Cκ0000000−1000Sκ0(τ−μ)00000000000−κC000100]

Now considering the nonlocal Eringen equation and replacing the strain term with the Eq. (6).

σ(e0a)22σx2=Y(e0+x1e1+x2e2){rr}σ−(e0a)2∂2σ∂x2=Y(e0+x1e1+x2e2){rr′}
(7)

By defining axial force to form N=σdAN=∫σdA and bended moment as M=xσdAM=∫xσdA, we will have:

×dAN(e0a)22Nx2=Ye0{rr}A×∫dA⇒N−(e0a)2∂2N∂x2=Ye0{rr′}A
(8)
×x1dAM1(e0a)22M1x2=Ye1{rr}I2×∫x1dA⇒M1−(e0a)2∂2M1∂x2=Ye1{rr′}I2
(9)
×x2dAM2(e0a)22M2x2=Ye2{rr}I1×∫x2dA⇒M2−(e0a)2∂2M2∂x2=Ye2{rr′}I1
(10)

Where I1=x22dAI1=∫x22dA and I2=x12dAI2=∫x12dA and {M1,M2}={x1,x2}σdA{M1,M2}=∫{x1,x2}σdA

For convenience, Eqs. (810) are brought into a matrix.

[NM1M2](e0a)2[NM1M2]=[Ye0AYe1I2Ye2I1]{rr}[NM1M2]−(e0a)2[N′′M′′1M′′2]=[Ye0AYe1I2Ye2I1]{rr′}
(11)

The GMDM model consists of two out of plane curved beams that are used to model a DNA. These two beams are connected with springs and dampers. By considering the mass of the nucleobases (Fig. 3b) and then by writing the strain energy and kinetic energy equations of the components, and the use of Navier-Stokes equations to apply the effects of a nucleoplasm, the effects of the temperature increase as an external work, and putting all of these equations in the Hamilton equation, the governing equation for the DNA model will be derived.

To derive the governing equations in the first step, we need to find the strain energy. Strain energy for two beams and also damper and spring connecting two beams will be as follows.

Π1=ΠOutofplanecurvednanobeam1=σ1ε1dA=σ1(e0+x1e1+x2e2){r1r1}dAdx3=(N1e0+M11e1+M12e2){r1r1}dx3Π1=ΠOutofplanecurvednanobeam1=∫σ1ε1dA=∫σ1(e0+x1e1+x2e2){r1r1′}dAdx3=∫(N1e0+M11e1+M12e2){r1r1′}dx3
(12)
Π2=ΠOutofplanecurvednanobeam2=σ2ε2dA=σ2(e0+x1e1+x2e2){r2r2}dAdx3=(N2e0+M21e1+M22e2){r2r2}dx3Π2=ΠOutofplanecurvednanobeam2=∫σ2ε2dA=∫σ2(e0+x1e1+x2e2){r2r2′}dAdx3=∫(N2e0+M21e1+M22e2){r2r2′}dx3
(13)
Π3=ΠTraction(spring)=12k(U1U2)2dx3=12k(NsR1NsR2)2dx3=12(r1r2)TK(r1r2)e2ωtdx3Π3=ΠTraction(spring)=12∫k(U1−U2)2dx3=12∫k(NsR1−NsR2)2dx3=12∫(r1−r2)TK(r1−r2)e2ωtdx3
(14)
Π4=ΠTraction(damper)=12ω(r1r2)TCa(r1r2)e2ωtdx3Π4=ΠTraction(damper)=12∫ω(r1−r2)TCa(r1−r2)e2ωtdx3
(15)

where:

Ns=[100010001000000000],K=[k000000k000000k000000000000000000000],Ca=[Ca000000Ca000000Ca000000000000000000000]Ns=[100000010000001000],K=[k000000k000000k000000000000000000000],Ca=[Ca000000Ca000000Ca000000000000000000000]

Finally, the strain energy of all the components is brought together and the strain energy of the whole system is obtained as

Π=Π1+Π2+Π3+Π4Π=Π1+Π2+Π3+Π4
(16)

For simplicity, Eqs. (12) and (13) can be demonstrated in the form of a matrix as the following:

Π2=[N2M21M22][e0e1e2]{r2r2}dx3=[N2M21M22]T[e0e1e2]{r2r2}dx3Π2=∫[N2M21M22][e0e1e2]{r2r2′}dx3=∫[N2M21M22]T[e0e1e2]{r2r2′}dx3
(17a)
Π1=[N1M11M12][e0e1e2]{r1r1}dx3=[N1M11M12]T[e0e1e2]{r1r1}dx3Π1=∫[N1M11M12][e0e1e2]{r1r1′}dx3=∫[N1M11M12]T[e0e1e2]{r1r1′}dx3
(17b)

It should be noted that in order to prepare the conditions for using variational method form, the matrix [e0e1e2]912[e0e1e2]9∗12 was separated and rearranged to this matrix [e01e11e21e02e12e22]9(6+6)[e01e02e11e12e21e22]9∗(6+6), in which:

e01=[0(τμ)Cκτμ0SκCκSκ0010100000],e01=[100010001000000000]e11=[000000000000CκSκ0(τμ)0κS],e12=[000000000000001010]e21=[000000000CκSκ00000(τμ)Cκ],e22=[000000000001000100]e01=[0τ−μ−Cκ0−10−(τ−μ)0Sκ100Cκ−Sκ0000],e01=[100000010000001000]e11=[0000Cκ(τ−μ)0000−Sκ000000−κS],e12=[0000000000010000−10]e21=[000−Cκ00000Sκ0(τ−μ)00000−Cκ],e22=[00000−1000000000100]

The kinetic energy of two beams and nucleobases with vibration frequency ωω is given by:

T1=TOutofplanecurvednanobeam1=ω22ρr1TAr1dx3T1=TOutofplanecurvednanobeam1=ω22∫ρr1TAr1dx3
(18a)
T2=TOutofplanecurvednanobeam2=ω22ρr2TAr2dx3T2=TOutofplanecurvednanobeam2=ω22∫ρr2TAr2dx3
(18b)
T1AT=TNukleobases(AT)=ω22(r1)Tm1(r1)dx3T1AT=TNukleobases(A−T)=ω22∫(r1)Tm1(r1)dx3
(18c)
T1CG=TNukleobases(GC)=ω22(r2)Tm2(r2)dx3T1CG=TNukleobases(G−C)=ω22∫(r2)Tm2(r2)dx3
(18d)
T2AT=TNukleobases(AT)=ω22(r1)Tm1(r1)dx3T2AT=TNukleobases(A−T)=ω22∫(r1)Tm1(r1)dx3
(18e)
T2CG=TNukleobases(GC)=ω22(r2)Tm2(r2)dx3T2CG=TNukleobases(G−C)=ω22∫(r2)Tm2(r2)dx3
(18f)
T=T1+T2+T1AT+T1CG+T2AT+T2CGT=T1+T2+T1AT+T1CG+T2AT+T2CG
(19)

where ρρ is the density of strands of DNA and:

A=[A000000A000000A000000I1000000I2000000J],AI1I2JS====bhx21dAx21dAI1+I2A=[A000000A000000A000000I1000000I2000000J],A=b∗hI1=∫x12dAI2=∫x12dAJS=I1+I2
m1m2==mAdenine+mThymine2mCytosine+mGuanine2m1=mAdenine+mThymine2m2=mCytosin⁡e+mGuanine2

It should be noted that in Fig. 3 and GMDM model, the mass of nucleobases have been considered. Adenine always provides hydrogen bond with Thymine and also Guanine always makes hydrogen bond with Cytosine. Therefore, by the averages of weight of Adenine and Thymine, also weight of Guanine and Cytosine, attach this average mass to the both beams. Depending on the genetic sequence in the DNA code, it is determined that which one of the nucleobases kinetic energy (T1AT,T1CG,T2AT,T2CGT1AT,T1CG,T2AT,T2CG) should be used.

The effects of the nucleoplasm on the vibration of DNA are also considered as an external work, which the Navier Stokes equations are also used to apply this effect. The effects of the nucleoplasm for one beam and for two directions x1x1 and x2x2 that are perpendicular to the cross-section are shown below:

ρn(U˙+UU)ρn(U˙+UU)==Px1+ρngx1+μvUPx2+ρngx2+μvUρn(U˙+UU′)=−∂P∂x1+ρngx1+μvU′′ρn(U˙+UU′)=−∂P∂x2+ρngx2+μvU′′
(20)

In which ρnP and μv are density of nucleoplasm, intracellular pressure and viscosity of nucleoplasm respectively.

The effects of fluid are considered as an external work.

WS1WS2==(Px2)T.As1.rdx3(Px1)T.As2.rdx3WS1=∫(∂P∂x2)T.As1.rdx3WS2=∫(∂P∂x1)T.As2.rdx3
(21)

In which:

AS1I1S1I2S1JS1====bLx22dAx23dAI1S1+I2S1AS1=[AS1000000AS1000000AS1000000I1S1000000I2S1000000JS1],AS1=b∗LI1S1=∫x22dAI2S1=∫x32dAJS1=I1S1+I2S1AS1=[AS1000000AS1000000AS1000000I1S1000000I2S1000000JS1],
AS2I1S2I2S2JS2====hLx23dAx21dAI1S2+I2S2AS2=[AS2000000AS2000000AS2000000I1S2000000I2S2000000JS2],AS2=h∗LI1S2=∫x32dAI2S2=∫x12dAJS2=I1S2+I2S2AS2=[AS2000000AS2000000AS2000000I1S2000000I2S2000000JS2],

Regardless of gravity and nonlinear term, the effects of fluid on DNA strands will be as follows:

W1S1=ρnr˙1.As1.r1dx3W1S1=−∫ρnr˙1.As1.r1dx3
(22a)
W1S2=ρnr˙1.As2.r1dx3W1S2=−∫ρnr˙1.As2.r1dx3
(22b)
W2S1=ρnr˙2.As1.r2dx3W2S1=−∫ρnr˙2.As1.r2dx3
(22c)
W2S2=ρnr˙2.As2.r2dx3W2S2=−∫ρnr˙2.As2.r2dx3
(22d)

where W1S1W1S1 represents the external work applied to number 1 strand in x2x2 directions and W2S1W2S1 represents the external work applied to number 2 strand in x1x1 directions. Also, the effects of temperature increase on DNA as linear in term of thickness of the beam will also be applied as an external work as below (since strands are larger than nucleobases, we neglected the effect of temperature on nucleobases).

WT1=l012NT(Ux3)2dx3WT1=∫0l12NT(∂U∂x3)2dx3
(23)

In which:

NT=h2h2AYdAα(TT0)dx1NT=∫−h2h2∬AYdAα(T−T0)dx1
(24)

By replacing the Eq. (24) in to the Eq. (23), we will have:

WT=l0((Nx1r1)TYαdAs2ΔT(Nx1r1))dx3WT=∫0l∬((∂N∂x1r1)TYαdAs2ΔT(∂N∂x1r1))dx3
(25)

The Eq. (25) can be written as follows:

WT=l0(rT1OT2YαdAs2ΔTO2r1)dx3WT=∫0l∬(r1TO2TYαdAs2ΔTO2r1)dx3
(26)

In which:

O2=Nx1=[000000000000001010]O2=∂N∂x1=[0000000000010000−10]

By substituting the strain energy (Eq. (16)) kinetic energy (Eq. (19)) external works (Eqs. (2126)) and also using variation method and put them in Hamilton relation, we will have:

δΠδTδW=0∫δΠ−δT−δW=0
δr1:([e01e11e21]T96[N1M11M12][e02e12e22]T96[N1M11M12])+K(r1r2)+(O2YAs2αΔTOT2)r1ω2(ρr1A+mKr1)+ω(Ca(r1r2)+ρnr1(As1+As2))=0δr1:([e01e11e21]9∗6T[N1M11M12]−[e02e12e22]9∗6T[N1′M11′M12′])+K(r1−r2)+(O2YAs2αΔTO2T)r1−ω2(ρr1A+mKr1)+ω(Ca(r1−r2)+ρnr1(As1+As2))=0
(27a)
δr2:(([e01e11e21]T96[N2M21M22][e02e12e22]T96[N2M21M22]))K(r1r2)(O2YAs2αΔTOT2)r2ω2(ρr2A+mKr2)+ω(Ca(r1r2)+ρnr2(As1+As2))=0δr2:(([e01e11e21]9∗6T[N2M21M22]−[e02e12e22]9∗6T[N2′M21′M22′]))−K(r1−r2)−(O2YAs2αΔTO2T)r2−ω2(ρr2A+mKr2)+ω(−Ca(r1−r2)+ρnr2(As1+As2))=0
(27b)

By merging Eq. (11) in the Eq. (27), the governing equations of DNA with considering the effects of the fluid and temperature change will be as:

([e01e11e21]T[Ye0AYe1I2Ye2I1][e02e12e22]T[Ye0AYe1I2Ye2I1](e0a)2([e01e11e21]T[Ye0AYe1I2Ye2I1]+2[e01e11e21]T[Ye0AYe1I2Ye2I1])){r1r1}([e02e12e22]T[Ye0AYe1I2Ye2I1]+2(e0a)2[e01e11e21]T[Ye0AYe1I2Ye2I1]){r1r1}+(K(r1r2)(e0a)2K(r1r