Rotational drag on DNA: a single molecule experiment

Within a single-molecule configuration, we have studied rotational drag on double stranded linear DNA by measuring the force during mechanical opening and closing of the double helix at different rates. The molecule is cranked at one end by the effect of unzipping and is free to rotate at the other end. In this configuration the rotational friction torque tau on double-stranded DNA leads to an additional contribution to the opening force. It is shown that the effect of rotational drag increases with the length of the molecule, is approximately proportional to the angular velocity of cranking, and we estimate that the torque tau is of the order of 1k(B)T for 10 000 base pairs of DNA cranked at 2000 turns per second.     

Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions

The adsorption dynamics of double-stranded DNA (dsDNA) molecules on a graphene oxide (GO) surface are important for applications of DNA/GO functional structures in biosensors, biomedicine and materials science. In this work, molecular dynamics simulations were used to examine the adsorption of different length dsDNA molecules (from 4 bp to 24 bp) on the GO surface. The dsDNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface. For short dsDNA (4 bp) molecules, the double-helix structure was partially or totally broken and the adsorption dynamics was affected by the structural fluctuation of short dsDNA and the distribution of the oxidized groups on the GO surface. For long dsDNA molecules (from 8 bp to 24 bp) adsorption is stable. By nonlinear fitting of the contact angle between the axis of the dsDNA molecule and the GO surface, we found that a dsDNA molecule adsorbed on a GO surface has the chance of orienting parallel to the GO surface if the length of the dsDNA molecule is longer than 54 bp. We attributed this behavior to the flexibility of dsDNA molecules. With increasing length, the flexibility of dsDNA molecules also increases, and this increasing flexibility gives an adsorbed dsDNA molecule more chance of reaching the GO surface with the free terminal. This work provides a whole picture of adsorption of dsDNA molecules on the GO surface and should be of benefit for the design of DNA/GO based biosensors.     

Non-hydrodynamic modes and general equations of state in lattice Boltzmann equations

The lattice Boltzmann equation is commonly used to simulate fluids with isothermal equations of state in a weakly compressible limit, and intended to approximate solutions of the incompressible Navier–Stokes equations. Due to symmetry requirements there are usually more degrees of freedom in the equilibrium distributions than there are constraints imposed by the need to recover the Navier–Stokes equations in a slowly varying limit. We construct equilibria for general barotropic fluids, where pressure depends only upon density, using the two-dimensional, nine velocity (D2Q9) and one-dimensional, five velocity (D1Q5) lattices, showing that one otherwise arbitrary function in the equilibria must be chosen to suppress instability.     

Internal mechanical response of a polymer in solution

We observed single molecules of fluorescently labeled double-stranded (ds) lambda DNA held in an anti-Brownian electrokinetic trap. From the measured density fluctuations we extract the density-density response function of the molecule over times >4.5 ms and distances >250 nm, i.e., how a perturbation in density in one part of the molecule propagates through the rest of the molecule. We find a nonmonotonic radial dependence of the relaxation time. In contrast with earlier measurements on freely diffusing dsDNA, we observe clear signs of internal hydrodynamic interactions.     

Direct Observation Method of Individual Single-Stranded DNA Molecules Using Fluorescent Replication Protein A

Direct observation studies of single molecules have revealed molecular behaviors usually hidden in the ensemble and time-averaging of bulk experiments. Direct single DNA molecule analysis of DNA metabolism reactions such as DNA replication, repair, and recombination is necessary to fully understand these essential processes. Intercalation of fluorescent dyes such as YOYO-1 and SYTOX Orange has been the standard method for observing single molecules of double-stranded DNA (dsDNA), but effective fluorescent dyes for observing single molecules of single-stranded DNA (ssDNA) have not been found. To facilitate direct single-molecule observations of DNA metabolism reactions, it is necessary to establish methods for discriminating ssDNA and dsDNA. To observe ssDNA directly, we prepared a fusion protein consisting of the 70 kDa DNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). This fusion protein had ssDNA-binding activity. In our experiments, dsDNA was stained by SYTOX Orange and ssDNA by RPA-YFP, and we succeeded in staining ssDNA and dsDNA by using RPA-YFP and SYTOX Orange simultaneously.     

Quantum Recoil Effects of Spontaneous Emission on Disentanglement

By taking into account spatial degrees of freedom of atoms, we study theinternal-state disentanglement dynamics of two atoms interacting with avacuum multi-mode noise field. We show that the complete internal-statedisentanglement of the two atoms, caused due to the atomic spontaneousemission can be achieved in a finite time.     

Dynamics of soft and semisoft nematic elastomers

We analyze analytically and numerically the dynamics of how a nematic elastomer-an anisotropic rubber-responds elastically and orientationally to an imposed strain. Because positional and orientational degrees of freedom are coupled, the response is not the simple exponential one might expect for a viscous system. Indeed, as a result of this nonlinear coupling, the different modes decay in two qualitatively different ways: with either two distinct or with the same exponential laws, depending, respectively, on whether there is or there is not complete reorientation of the molecular long axes. In addition, at the special values of the strain that form the boundaries between different equilibrium behaviors, relaxation is much slower, i.e., it follows a power law.     

Effect of Laser Field and Mechanical Force on Deoxyribonucleic Acid Melting

We propose a physics method to study the effect of laser field and mechanical force on the melting process of double-stranded deoxyribonucleic acid （DNA）. A two-dimensional lattice model is established for DNA molecules stuck on the surface, and the stretching energy of the hydrogen bond and stacking energy for each DNA molecule are calculated by using a nonlinear potential. A real-time algorithm is employed to deal with the dynamics process of DNA melting. Numerical results explain the experimental observations. The spatial distribution of the laser field determines the sequences of DNA melting. The simulation has shown the dependence of the final number of melted DNA on the laser field and mechanical force.     

Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules

We obtain, using transfer-matrix methods, the distribution function P(R) of the end-to-end distance, the loop formation probability, and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the appearance of "bubbles," localized regions of enhanced flexibility associated with the opening of a few base pairs of double-stranded DNA in thermal equilibrium, leads to dramatic changes in P(R) and unusual force-extension curves. An analytic formula for the loop formation probability in the presence of bubbles is proposed. For short heterogeneous chains, we demonstrate a strong dependence of loop formation probabilities on sequence.     

The temperature jump and slow evaporation in molecular gases

We set up model transport equations that describe the behavior of molecular (diatomic and polyatomic) gases with a molecule collision rate proportional to the molecular velocity. In deriving these equations we allow for the internal (rotational) degrees of freedom, while the vibrational degrees of freedom are assumed “frozen.” We also set up an exact equation for the problem of the temperature jump with allowance for slow evaporation from the liquid surface into the saturated vapor atmosphere. Finally, we derive explicit formulas for calculating the coefficients of the temperature jump and gas-density jump above a flat surface and do the necessary numerical calculations. Zh. éksp. Teor. Fiz. 114, 956–971 (September 1998)     

Unzipping kinetics of double-stranded DNA in a nanopore

We studied the unzipping of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. Polymerase chain reaction analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip each molecule was inferred from the ionic current signature of DNA traversal. The distribution of times to unzip under various experimental conditions fit a simple kinetic model. Using this model, we estimated the enthalpy barriers to unzipping and the effective charge of a nucleotide in the pore, which was considerably smaller than previously assumed.     

Rovibrational excitation within the infinite conical well: Desorption of diatomic molecules

An analytic model for the hindered rotational states of a diatomic molecule adsorbed upright on a solid surface is discussed. Various model dynamics situations, within the sudden approximation, designed to simulate desorption are presented and rotational state distributions are calculated including both rotational and translational degrees of freedom. Criteria are established for observing rotationally cool desorbed molecules.     

Biaxial nematic phase in the Maier-Saupe model for a mixture of discs and cylinders

We analyze the global phase diagram of a Maier-Saupe lattice model with the inclusion of shape-disordered degrees of freedom to mimic a mixture of oblate and prolate molecules (discs and cylinders). In the neighborhood of a Landau multicritical point, solutions of the statistical problem can be written as a Landau-de Gennes expansion for the free energy. If the shape-disordered degrees of freedom are quenched, we confirm the existence of a biaxial nematic structure. If orientational and disorder degrees of freedom are allowed to thermalize, this biaxial solution becomes thermodynamically unstable. Also, we use a two-temperature formalism to mimic the presence of two distinct relaxation times, and show that a slight departure from complete thermalization is enough to stabilize a biaxial nematic phase.     

Cavity cooling of internal molecular motion

We predict that it is possible to cool rotational, vibrational, and translational degrees of freedom of molecules by coupling a molecular dipole transition to an optical cavity. The dynamics is numerically simulated for a realistic set of experimental parameters using OH molecules. The results show that the translational motion is cooled to a few muK and the internal state is prepared in one of the two ground states of the two decoupled rotational ladders in a few seconds. Shorter cooling times are expected for molecules with larger polarizability.     

Biophysical characterization of DNA binding from single molecule force measurements

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.     

Core level photoemission evidence of frustrated surface molecules: a germ of disorder at the (111) surface of C60 before the order-disorder surface phase transition

Using high resolution core level photoemission, we investigated the disordering transition of the fullerene molecules at the (111) surface of C (60) films. The experimental evidence of a two-step mechanism for the rotational disordering of surface fullerene molecules is provided. The data are consistent with a recent model in which the rotational degrees of freedom of one molecule, out of the four inequivalent C (60) molecules of the low temperature (2x2) surface unit cell, melt about 100 K before the bulk phase transition.     

Structure and Dynamics of dsDNA in Cell-like Environments

Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.     

Vibrational-rotational behavior of diatomic heteronuclear molecular systems in intense laser pulses

The dynamics of diatomic heteronuclear molecules in the low-frequency intense laser pulses is studied by numerical solution of the time-dependent Schr?dinger equation and both rotational and vibrational degrees of freedom are taken into account. The interference stabilization against the dissociation process is found to take place in a strong field and is shown to result in trapping of population in different rotational-vibrational bound states due to efficient Raman V- and ??-type transitions. The interplay between the vibrational and rotational dynamics of a molecule is investigated. The dissociation suppression due to the interference mechanism and all its attributes are established in the case of multiphoton coupling between the initial state and dissociation continuum.