Chain length of closed circle DNA is equal. The same closed circle DNA＇s position corresponds to different recognition sequence, and the same recognition sequence corresponds to different foreign DNA segment, so clos...Chain length of closed circle DNA is equal. The same closed circle DNA＇s position corresponds to different recognition sequence, and the same recognition sequence corresponds to different foreign DNA segment, so closed circle DNA computing model is generalized. For change positive-weighted Hamilton circuit problem, closed circle DNA algorithm is put forward. First, three groups of DNA encoding are encoded for all arcs, and deck groups are designed for all vertices. All possible solutions are composed. Then, the feasible solutions are filtered out by using group detect experiment, and the optimization solutions are obtained by using group insert experiment and electrophoresis experiment. Finally, all optimization solutions are found by using detect experiment. Complexity of algorithm is concluded and validity of DNA algorithm is explained by an example. Three dominances of the closed circle DNA algorithm are analyzed, and characteristics and dominances of group delete experiment are discussed.展开更多
In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal a...In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal and electrical properties of DNA biofilm. In this paper, the elastic properties of dsDNA biofilm are studied. First, the Parsegian＇s empirical potential based on a mesoscopic liq- uid crystal theory is employed to describe the interaction energy among coarse-grained DNA cylinders. Then, con- sidering a Gaussian distribution of DNA interaxial distance, the thought experiment method is used to derive an analyti- cal expression for Young＇s modulus of DNA biofilm with a stochastic packing pattern for the first time. Results show that Young＇s modulus of DNA biofilm is on the order of 10 MPa. These findings could provide a simple and effective method to evaluate the mechanical properties of soft biofilm on snbstrate.展开更多
Alzheimer’s disease（AD）is the most common type of dementia in elderly population.With a growing aging population not only in the United States but also in the worldwide,AD constitutes an emergent public health prob...Alzheimer’s disease（AD）is the most common type of dementia in elderly population.With a growing aging population not only in the United States but also in the worldwide,AD constitutes an emergent public health problem.展开更多
Background： Sperm DNA fragmentation（sDF） has been proved to be an important parameter in order to predict in vitro the potential fertility of a semen sample. Colloid centrifugation could be a suitable technique to ...Background： Sperm DNA fragmentation（sDF） has been proved to be an important parameter in order to predict in vitro the potential fertility of a semen sample. Colloid centrifugation could be a suitable technique to select those donkey sperm more resistant to DNA fragmentation after thawing. Previous studies have shown that to elucidate the latent damage of the DNA molecule, sDF should be assessed dynamically, where the rate of fragmentation between treatments indicates how resistant the DNA is to iatrogenic damage. The rate of fragmentation is calculated using the slope of a linear regression equation. However, it has not been studied if s DF dynamics fit this model. The objectives of this study were to evaluate the effect of different after-thawing centrifugation protocols on sperm DNA fragmentation and elucidate the most accurate mathematical model（linear regression, exponential or polynomial） for DNA fragmentation over time in frozen-thawed donkey semen.Results： After submitting post-thaw semen samples to no centrifugation（UDC）, sperm washing（SW） or single layer centrifugation（SLC） protocols, sD F values after 6 h of incubation were significantly lower in SLC samples than in SW or UDC.Coefficient of determination（R-2） values were significantly higher for a second order polynomial model than for linear or exponential. The highest values for acceleration of fragmentation（aSDF） were obtained for SW, fol owed by SLC and UDC.Conclusion： SLC after thawing seems to preserve longer DNA longevity in comparison to UDC and SW. Moreover,the fine-tuning of models has shown that sDF dynamics in frozen-thawed donkey semen fit a second order polynomial model, which implies that fragmentation rate is not constant and fragmentation acceleration must be taken into account to elucidate hidden damage in the DNA molecule.展开更多
There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is studied under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The ther...There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is studied under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The thermodynamics analysis using the transfer integral operator method is briefly reviewed. In particular, the lattice size is discussed and a conjecture about the minimum energy to denaturation is proposed. In terms of the dynamical aspects of the model, the equations of motion for the system are integrated and the results determine the energy density where the denatura- tion occurs. The behavior of the lattice near the phase transition is analyzed. The relation between the thermodynamical and dynamical results is discussed.展开更多
The influence of power-low long-range interactions （LRI） and helicoidal coupling （HC） on the properties of localized solitons in a DNA molecule when a ribonucleic acid polymerase （RNAP） binds to it at the physio...The influence of power-low long-range interactions （LRI） and helicoidal coupling （HC） on the properties of localized solitons in a DNA molecule when a ribonucleic acid polymerase （RNAP） binds to it at the physiological temperature is analytically and numerically investigated in this paper. We have made an analogy with the Heisenberg model Hamiltonian of an anisotropic spin ladder with ferromagnetic legs and anti-ferromagnetic rung coupling. When we limit ourselves to the second-order terms in the Taylor expansion, the DNA dynamics is found to be governed by a completely integrable nonlinear Schr？dinger （NLS） equation. In this case, results show that increasing the value of HC force or LRI parameter enhances the bubble height and reduces the number of base pairs which form the bubble. For the fourth-order terms in a Taylor expansion, results are closely resembling those of second-order terms, and are confirmed by numerical investigation. These results match with some experimental data and thus provide a better representation of the base pairs opening in DNA which is essential for the transcription process.展开更多
The objective of this paper is to apply the improved generalized Riccati equation mapping method to find many families of exact traveling wave solutions for the general nonlinear dynamic system in a new double-chain m...The objective of this paper is to apply the improved generalized Riccati equation mapping method to find many families of exact traveling wave solutions for the general nonlinear dynamic system in a new double-chain model of DNA. This model consists of two long elastic homogeneous strands connected with each other by an elastic membrane. Hyperbolic and trigonometric function solutions of this model are obtained. Comparison between our results and the well-known results are given.展开更多
Deoxyribonucleic acid(DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded(ss) strands, forming a double-stranded(ds) DNA with a right-handed double-helical confo...Deoxyribonucleic acid(DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded(ss) strands, forming a double-stranded(ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.展开更多
The central dogma of molecular biology describes the flow of genetic information from DNA via RNA to protein and duplication from ancestral to descendent DNA（Crick,1958）.However,the genetic information could not be ...The central dogma of molecular biology describes the flow of genetic information from DNA via RNA to protein and duplication from ancestral to descendent DNA（Crick,1958）.However,the genetic information could not be quantified and mathematically modeled.So it differs from the“information”formulated by Shannon and used in information and coding theories（Shannon,1949）.展开更多
基金supported by the National Natural Science Foundation of China(60574041)the Natural ScienceFoundation of Hubei Province(2007ABA407).
文摘Chain length of closed circle DNA is equal. The same closed circle DNA＇s position corresponds to different recognition sequence, and the same recognition sequence corresponds to different foreign DNA segment, so closed circle DNA computing model is generalized. For change positive-weighted Hamilton circuit problem, closed circle DNA algorithm is put forward. First, three groups of DNA encoding are encoded for all arcs, and deck groups are designed for all vertices. All possible solutions are composed. Then, the feasible solutions are filtered out by using group detect experiment, and the optimization solutions are obtained by using group insert experiment and electrophoresis experiment. Finally, all optimization solutions are found by using detect experiment. Complexity of algorithm is concluded and validity of DNA algorithm is explained by an example. Three dominances of the closed circle DNA algorithm are analyzed, and characteristics and dominances of group delete experiment are discussed.
基金supported by the National Natural Science Foundation of China(11272193 and 10872121)the Shanghai Leading Academic Discipline Project(S30106)
文摘In microcantilever-based label-free biodetection technologies, deflection changes induced by adsorptions of double-stranded DNA （dsDNA） molecules on Au-layer surface are greatly affected by the mechanical, thermal and electrical properties of DNA biofilm. In this paper, the elastic properties of dsDNA biofilm are studied. First, the Parsegian＇s empirical potential based on a mesoscopic liq- uid crystal theory is employed to describe the interaction energy among coarse-grained DNA cylinders. Then, con- sidering a Gaussian distribution of DNA interaxial distance, the thought experiment method is used to derive an analyti- cal expression for Young＇s modulus of DNA biofilm with a stochastic packing pattern for the first time. Results show that Young＇s modulus of DNA biofilm is on the order of 10 MPa. These findings could provide a simple and effective method to evaluate the mechanical properties of soft biofilm on snbstrate.
基金supported by the Brazilian funding agencies:CNPq(Conselho Nacional de Desenvolvimento Científico e Tecnológico)CAPES(Coordenacao de Aperfeicoamento de Pessoal de Nível Superior)-No:5614112Student Agreement Program for post graduation–PEC-PG.
文摘Alzheimer’s disease（AD）is the most common type of dementia in elderly population.With a growing aging population not only in the United States but also in the worldwide,AD constitutes an emergent public health problem.
基金partially supported by grants RZ2009-00006-00-00(Instituto Nacional de Investigacion y Tecnología Agraria y Alimentaria,Ministerio de Ciencia e Innovación,Spain)AGL-2013-42726-R(Secretaria de Estado de Investigacion,Desarrollo e Innovacion,Ministerio de Economia y Competitividad,Spain)+1 种基金supported by a Ph.D.fellowship from the ceiA3(Andalucia,Spain)with funding provided by Banco Santander through its Global Division,Santander Universidadesfunded by the Swedish Foundation for Equine Research,Stockholm,Sweden(H14-47-008)
文摘Background： Sperm DNA fragmentation（sDF） has been proved to be an important parameter in order to predict in vitro the potential fertility of a semen sample. Colloid centrifugation could be a suitable technique to select those donkey sperm more resistant to DNA fragmentation after thawing. Previous studies have shown that to elucidate the latent damage of the DNA molecule, sDF should be assessed dynamically, where the rate of fragmentation between treatments indicates how resistant the DNA is to iatrogenic damage. The rate of fragmentation is calculated using the slope of a linear regression equation. However, it has not been studied if s DF dynamics fit this model. The objectives of this study were to evaluate the effect of different after-thawing centrifugation protocols on sperm DNA fragmentation and elucidate the most accurate mathematical model（linear regression, exponential or polynomial） for DNA fragmentation over time in frozen-thawed donkey semen.Results： After submitting post-thaw semen samples to no centrifugation（UDC）, sperm washing（SW） or single layer centrifugation（SLC） protocols, sD F values after 6 h of incubation were significantly lower in SLC samples than in SW or UDC.Coefficient of determination（R-2） values were significantly higher for a second order polynomial model than for linear or exponential. The highest values for acceleration of fragmentation（aSDF） were obtained for SW, fol owed by SLC and UDC.Conclusion： SLC after thawing seems to preserve longer DNA longevity in comparison to UDC and SW. Moreover,the fine-tuning of models has shown that sDF dynamics in frozen-thawed donkey semen fit a second order polynomial model, which implies that fragmentation rate is not constant and fragmentation acceleration must be taken into account to elucidate hidden damage in the DNA molecule.
基金grateful to Capes and CNPq for the financial support.
文摘There are several mechanical models to describe the DNA phenomenology. In this work the DNA denaturation is studied under thermodynamical and dynamical point of view using the well known Peyrard-Bishop model. The thermodynamics analysis using the transfer integral operator method is briefly reviewed. In particular, the lattice size is discussed and a conjecture about the minimum energy to denaturation is proposed. In terms of the dynamical aspects of the model, the equations of motion for the system are integrated and the results determine the energy density where the denatura- tion occurs. The behavior of the lattice near the phase transition is analyzed. The relation between the thermodynamical and dynamical results is discussed.
文摘The influence of power-low long-range interactions （LRI） and helicoidal coupling （HC） on the properties of localized solitons in a DNA molecule when a ribonucleic acid polymerase （RNAP） binds to it at the physiological temperature is analytically and numerically investigated in this paper. We have made an analogy with the Heisenberg model Hamiltonian of an anisotropic spin ladder with ferromagnetic legs and anti-ferromagnetic rung coupling. When we limit ourselves to the second-order terms in the Taylor expansion, the DNA dynamics is found to be governed by a completely integrable nonlinear Schr？dinger （NLS） equation. In this case, results show that increasing the value of HC force or LRI parameter enhances the bubble height and reduces the number of base pairs which form the bubble. For the fourth-order terms in a Taylor expansion, results are closely resembling those of second-order terms, and are confirmed by numerical investigation. These results match with some experimental data and thus provide a better representation of the base pairs opening in DNA which is essential for the transcription process.
文摘The objective of this paper is to apply the improved generalized Riccati equation mapping method to find many families of exact traveling wave solutions for the general nonlinear dynamic system in a new double-chain model of DNA. This model consists of two long elastic homogeneous strands connected with each other by an elastic membrane. Hyperbolic and trigonometric function solutions of this model are obtained. Comparison between our results and the well-known results are given.
基金supported by the Fundamental Research Funds for the Central Universities(Grant No.2013121005)the National Natural Science Foundation of China(Grant Nos.11474237 and 11574310)+1 种基金the 111 Project (Grant No.B16029)the National Research Foundation of Singapore through the NRF Investigatorship and the Mechanobiology Institute
文摘Deoxyribonucleic acid(DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded(ss) strands, forming a double-stranded(ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.
基金supported by the National Natural Science Foundation of China (31372222)the Key Research Project of the National Natural Science Foundation of China (91531302)
文摘The central dogma of molecular biology describes the flow of genetic information from DNA via RNA to protein and duplication from ancestral to descendent DNA（Crick,1958）.However,the genetic information could not be quantified and mathematically modeled.So it differs from the“information”formulated by Shannon and used in information and coding theories（Shannon,1949）.
