Electronic transport in double-strand poly(dG)-poly(dC) DNA segments

We study the electronic properties of a double-strand quasiperiodic DNA molecule modeled by a one-dimensional effective Hamiltonian, which includes contributions from the nucleobasis system as well as the sugar-phosphate backbone. Our theoretical approach makes use of Dyson's equation together with a transfer-matrix treatment, considering an electronic tight-binding Hamiltonian model to investigate the electronic density of states (DOS) and the electronic transmissivity of sequences of DNA finite segments. To mimic the DNA segments, we consider the finite quasiperiodic sequences of Fibonacci's type, in a poly(dG)-poly(dC) configuration, whose building blocks are the bases guanine G and cytosine C. We compared the electronic transport found for the quasiperiodic structure to those using a sequence of natural DNA, as part of the human chromosome Ch22.     

Temperature dependence of transport behavior of a short DNA molecule

DNA molecules may work as novel devices due to their interesting electronic transport properties. We here propose a theoretical method to deal with the temperature dependence of the transport behavior of a short DNA molecule, taking into account Coulomb interaction of electrons and the coupling between electrons and the two-level system in the DNA molecule. The nonlinear current-voltage curves are derived by using the Landauer formulae. We find that the voltage gap of the current-voltage curves is sensitive to the parameters of the two-level system. We also find that Coulomb blockade peaks can be controlled by varying the temperature, which relates to particular features of the DNA molecule.     

Thermal Vibration and Twist Induced Semiconducting Behaviour in Short DNA Wires

We study the transport properties of electrons in a short homogeneous DNA molecule where thermal vibrations and twist fluctuations of the base molecules are considered. The nonlinear current-voltage curves can be derived by using the equivalent single-particle multichannel network. The voltage gap is sensitive to the strength of thermal vibrations and twist fluctuations of the base molecules. Our results are in good agreement with the recent finding of semiconducting behaviour in short poly（G）-poly（C） DNA oligomers. The present method can also be used to calculate the other molecular wires.     

Effects of interbase electronic coupling and electrode on charge transport through short DNA molecules: A numerical study

We report on theoretical results about the coherent charge transport of short DNA molecules using the transmission approach, as a function of interbase electronic coupling and electrodes. A dinucleotide poly(GC) chain is studied as a generic case, and the transmission coefficient as well as I–V$I\text{–}V$ curves are presented. The well-stacked “π  -way” is favorable for conveying charge carriers through short sequences, and the current can be reduced in strong electronic coupling regime. Further, the steplike appearance and threshold voltage in I–V$I\text{–}V$ curves dramatically depend on the coupling strength. The electrodes are shown to dominate charge transport of single band and may contribute to the threshold voltage, and the enhancement of conductance in low contact coupling regime is possible.     

Lie Symmetries and Conserved Quantities for Super-Long Elastic Slender Rod

DNA is a nucleic acid molecule with double-helical structures that are special symmetrical structures attracting great attention of numerous researchers. The super-long elastic slender rod, an important structural model of DNA and other long-train molecules, is a useful tool in analysing the symmetrical properties and the stabilities of DNA. We study the Lie symmetries of a super-long elastic slender rod by using the methods of infinitesimal transformation. Based on Kirchhoff＇s analogue, generalized Hamilton canonical equations are analysed. The infinitesimal transformations with respect to the radian coordinate, the generalized coordinate, and the quasimomentum of the model are introduced. The Lie symmetries and conserved quantities of the model are presented.     

Nonlinear Schrödinger equation and DNA dynamics

We study a possible solitary wave solution of the nonlinear Schrödinger equation (NLSE). It is shown that the wave can be both modulated and nonmodulated depending on a ratio of the envelope and the carrier wave velocities. We also study the same type of the soliton solution in DNA dynamics. We show that the ratio of these two velocities is a measure of modulation and we conclude that the modulated wave is more stable than the nonmodulated one. Finally, we solved the problem concerning three parameters arising from the applied procedure for the solution of the NLSE.     

Transport and magnetic properties of disordered LixVyO2 (x=0.8 and y=0.8)

The magnetic and electron transport properties of rhombohedral Li_xV_yO₂ (x=0.8 and y=0.8) are studied. The dc susceptibility of Li_xV_yO₂ can be well fitted to the modified Curie-Weiss law, which verified the paramagnetic ground state. The magnetic hysteresis and ac susceptibility also confirm this paramagnetism. The Li_xV_yO₂ exhibits semiconducting behavior, which is explained by thermal activated process at high temperature and variable-range hopping mechanism at low temperature. Anderson localization plays an important role in both the electron transport behavior and the magnetic behavior due to the site disorder between the Li⁺ ion and V⁴⁺ ion.     

Parameter selection in a Peyrard-Bishop-Dauxois model for DNA dynamics

In this Letter we study possible intervals for some parameters existing in the Peyrard-Bishop-Dauxois (PBD) model for the DNA dynamics. These parameters describe longitudinal and helicoidal interactions between nucleotides and a Morse potential approximating transverse interactions. We also estimate a possible interval for a wave number of a carrier component of a modulated solitonic wave. Finally, we compare our statements with experimental value of solitonic velocity in DNA.     

Low-temperature resistance of DNA-templated nanowires

We present low-temperature measurements of the electrical conductivity of metallic nanowires assembled on single DNA molecules by chemical deposition of a thin continuous palladium film. The investigated nanowires exhibit ohmic transport behaviour at room temperature. At low temperature we observe an increase of resistance with decreasing temperature that follows a logarithmic dependence. This behaviour can be described with quantum effects in a disordered metallic film. Received: 4 October 2001 / Accepted: 12 December 2001 / Published online: 20 March 2002     

DNA dynamics - Experiment proposals

We argue that a breather wave, describing DNA dynamics, behaves like a real soliton. We rely on a Peyrard-Bishop-Dauxois (PBD) model. In addition, we propose a couple of experiments to confirm or reject this statement. These experiments should study solitonic interactions using micromanipulation technique. Also, we suggest how to measure a solitonic width and its amplitude.     

In vivo bone regeneration using a novel porous bioactive composite

Many commercial bone graft substitutes (BGS) and experimental bone tissue engineering scaffolds have been developed for bone repair and regeneration. This study reports the in vivo bone regeneration using a newly developed porous bioactive and resorbable composite that is composed of bioactive glass (BG), collagen (COL), hyaluronic acid (HYA) and phosphatidylserine (PS), BG-COL-HYA-PS. The composite was prepared by a combination of sol-gel and freeze-drying methods. A rabbit radius defect model was used to evaluate bone regeneration at time points of 2, 4 and 8 weeks. Techniques including radiography, histology, and micro-CT were applied to characterize the new bone formation. 8 weeks results showed that (1) nearly complete bone regeneration was achieved for the BG-COL-HYA-PS composite that was combined with a bovine bone morphogenetic protein (BMP); (2) partial bone regeneration was achieved for the BG-COL-HYA-PS composites alone; and (3) control remained empty. This study demonstrated that the novel BG-COL-HYA-PS, with or without the grafting of BMP incorporation, is a promising BGS or a tissue engineering scaffold for non-load bearing orthopaedic applications.     

Counterion vibrations in the DNA low-frequency spectra

The vibrations of univalent metal cations with respect to phosphate groups of the DNA backbone are described using the four-mass model approach (S.N. Volkov, S.N. Kosevich, J. Biomol. Struct. Dyn. 8, 1069 (1991)) extended in this paper. The force constant of the counterion-phosphate interaction is determined by considering the DNA with counterions as a lattice of ion crystal. For such ion-phosphate lattice the Madelung constant and the dielectric constant are estimated. The obtained value of the Madelung constant is lower than for the NaCl crystal, and its value is about 1.3. The dielectric constant is within 2.3-2.7 depending on the counterion type and form of the double helix. The calculations of the low-frequency spectra show that for the DNA with metal cations Na⁺ , K⁺ , Rb⁺ and Cs⁺ the frequency of ion-phosphate vibrations decreases from 174 to 96cm^-1 as the counterion mass increases. The obtained frequencies agree well with the vibrational spectra of polynucleotides in a dry state which prove our suggestion about the existence of the ion-phosphate lattice around the DNA double helix. The amplitudes of conformational vibrations for DNA in B -form are calculated as well. The results demonstrate that light counterions ( Na⁺ do not disturb the internal dynamics of the DNA. However, heavy counterions ( Cs⁺ have effect on the internal vibrations of the DNA structural elements.     

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system, one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational heat resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process.     

Structural class tendency of polypeptide: A new conception in predicting protein structural class

Prediction of protein domain structural classes is an important topic in protein science. In this paper, we proposed a new conception: structural class tendency of polypeptides (SCTP), which is based on the fact that a given amino acid fragment tends to be presented in certain type of proteins. The SCTP is obtained from an available training data set PDB40-B. When using the SCTP to predict protein structural classes by Intimate Sorting predictive method, we got the predictive accuracy (jackknife test) with 93.7%, 96.5%, and 78.6% for the testing data set PDB40-j, Chou&Maggiora and CHOU. These results indicate that the SCTP approach is quite encouraging and promising. This new conception provides an effective tool to extract valuable information from protein sequences.     

A study of Barstar folding events using boundary value simulations

From extensive biophysical studies of protein folding, two competing mechanisms emerged: hydrophobic collapse and the framework model. Our protein of choice is Barstar—a barnase inhibitor. The approximation algorithm we used to study Barstar folding trajectories is called SDEL—stochastic difference equation in length. Using the native structure as the final boundary value and a collection of unfolded structures as the varying initial boundary value, SDEL calculates an ensemble of least action pathways between these boundaries. The results are atomically detailed folding pathways, with as many intermediate structures as you request in the input. We generated 12 pathways, starting from a structurally wide selection of unfolded conformations. Using the protein's radius of gyration as our primary reaction coordinate, we tracked H-bonds, dihedral angles, native and non-native contacts, and energy along the folding pathways. This paper will follow our findings, with special emphasis on pinpointing hydrophobic collapse as a more appropriate mechanism for Barstar. Comparison with pathway predictions for Barstar using experimental techniques will also be discussed.     

Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences

In this work, we consider the critical force required to unzip two different naturally occurring sequences of double-stranded DNA (dsDNA) at temperatures ranging from 20 ^°C to 50 ^°C, where one of the sequences has a 53% average guanine-cytosine (GC) content and the other has a 40% GC content. We demonstrate that the force required to separate the dsDNA of the 53% GC sequence into single-stranded DNA (ssDNA) is approximately 0.5 pN, or approximately 5% greater than the critical force required to unzip the 40% GC sequence at the same temperature. In the temperature range between 20 and 40 ^°C the measured critical forces correspond reasonably well to predictions based on a simple theoretical homopolymeric model, but at temperatures above 40 ^°C the measured critical forces are much smaller than the predicted forces. The correspondence between theory and experiment is not improved by using Monte Carlo simulations that consider the heteropolymeric nature of the sequences.     

Strategies for the separation of polyelectrolytes based on non-linear dynamics and entropic ratchets in a simple microfluidic device

We perform Monte Carlo simulations of an existing electrophoretic microchannel device used for the size separation of large DNA fragments. This device is normally operated with a constant (dc) driving field. In contrast, we consider the case of a varying (ac) driving field, in the zero-frequency limit. We find that a time-asymmetric pulse can yield interesting migration regimes, in particular bidirectional transport for different molecular sizes. We also study a spatially asymmetric version of the device and show that it can rectify unbiased but non-equilibrium molecular motion, in agreement with previous predictions for entropic ratchets. Finally, at finite frequency we uncover a resonance for the molecular velocity in the channel which could lead to improved performance. Received: 16 November 2001 / Accepted: 11 February 2002 / Published online: 22 April 2002     

Comment on the paper “Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences” by C.H. Lee, C. Danilowicz, V.W Coljee, and M. Prentiss

The paper by Lee et al. describes the experiments on the unzipping of λ DNA sequences as a function of force and temperature. This comment aims to stress that the unzipping takes place out of equilibrium due to high sequence-dependent free-energy barriers. The force at which a heterogeneous sequence is unzipped therefore depends on the experimental waiting time.     

Low-temperature specific heat spectra considering nonextensive long-range correlated quasiperiodic DNA molecules

We consider the low-temperature specific heat spectra of long-range correlated quasiperiodic DNA molecules using a q-gaussian distribution, and compare them with those considering the Boltzmann-Gibbs distribution. The energy spectra are calculated using the one-dimensional Schrödinger equation in a tight-binding approximation with the on-site energy exhibiting long-range disorder and non-random hopping amplitudes. We focus our attention at the low temperature region, where the specific heat spectra presents a logarithmic-periodic oscillations as a function of the temperature T around a mean value given by a characteristic dimension of the energy spectrum.     

Investigation of Chlorophyll Protein 43 and 47 Denaturation by Terahertz Time-Domain Spectroscopy

We demonstrate the applications of terahertz time-domain spectroscopy to distinguish conformation changes of the chlorophyll proteins CP43 and CP47 induced by the treatment of guanidine hydrochloride, light irradiation and heating. It is indicated that THz transmission spectroscopy can be used for monitoring protein denaturation and associated conformation change processes in a feasible and effective way.