Probing DNA conformational changes with high temporal resolution by Tethered Particle Motion

The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150~nm). Notably we demonstrate that, for a particle of radius 20~nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20~ms.Comment: Improved version, to appear in Physical Biology. 10 pages + 10 pages of supporting materia

Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer

Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a Schr\"{o}dinger equation variationally. Theoretical results based on this model on the extension versus force and extension versus degree of supercoiling relations of DNA chain are in good agreement with the experimental observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it ibid.} {\bf 271}, 1835 (1996)].Comment: 8 pages in Revtex format, with 4 EPS figure

Critical exponents at the ferromagnetic transition in tetrakis(diethylamino)ethylene-C60_{60} (TDAE-C60_{60})

Critical exponents at the ferromagnetic transition were measured for the first time in an organic ferromagnetic material tetrakis(dimethylamino)ethylene fullerene[60] (TDAE-C$_{60}$). From a complete magnetization-temperature-field data set near $T_{c}=16.1\pm 0.05,$ we determine the susceptibility and magnetization critical exponents $\gamma =1.22\pm 0.02$ and $\beta =0.75 \pm 0.03$ respectively, and the field vs. magnetization exponent at $T_{c}$ of $\delta =2.28\pm 0.14$. Hyperscaling is found to be violated by $\Omega \equiv d^{\prime}-d \approx -1/4$, suggesting that the onset of ferromagnetism can be related to percolation of a particular contact configuration of C$_{60}$ molecular orientations.Comment: 5 pages, including 3 figures; to appear in Phys. Rev. Let

Probing complex RNA structures by mechanical force

RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by solely invoking successive openings of native helices. Indeed, typical force-extension responses of complex RNA molecules are largely shaped by stretching-induced, long-lived intermediates including non-native helices. This is first shown for a set of generic structural motifs found in larger RNA structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA, which exhibits a surprisingly well-structured and reproducible unfolding pathway under mechanical stretching. Using out-of-equilibrium stochastic simulations, we demonstrate that these experimental results reflect the slow relaxation of RNA structural rearrangements. Hence, micromanipulations of single RNA molecules probe both their native structures and long-lived intermediates, so-called "kinetic traps", thereby capturing -at the single molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure

Mechanical response of plectonemic DNA: an analytical solution

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact pressure, twisting moment and geometrical parameters of the supercoiled region. We apply our model to magnetic tweezer experiments of a DNA molecule subjected to a tensile force and a torque, and extract mechanical and geometrical quantities from the linear part of the experimental response curve. These reconstructed values are derived in a self-contained manner, and are found to be consistent with those available in the literature.Comment: 14 pages, 4 figure

Gate-induced band ferromagnetism in an organic polymer

We propose that a chain of five-membered rings (polyaminotriazole) should be ferromagnetic with an appropriate doping that is envisaged to be feasible with an FET structure. The ferromagnetism is confirmed by a spin density functional calculation, which also shows that ferromagnetism survives the Peierls instability. We explain the magnetism in terms of Mielke and Tasaki's flat-band ferromagnetism with the Hubbard model. This opens a new possibility of band ferromagnetism in purely organic polymers.Comment: 4 pages, 7 figure

A DMRG Study of Low-Energy Excitations and Low-Temperature Properties of Alternating Spin Systems

We use the density matrix renormalization group (DMRG) method to study the ground and low-lying excited states of three kinds of uniform and dimerized alternating spin chains. The DMRG procedure is also employed to obtain low-temperature thermodynamic properties of these systems. We consider a 2N site system with spins $s_1$ and $s_2$ alternating from site to site and interacting via a Heisenberg antiferromagnetic exchange. The three systems studied correspond to $(s_1 ,s_2 )$ being equal to $(1,1/2),(3/2,1/2)$ and $(3/2,1)$; all of them have very similar properties. The ground state is found to be ferrimagnetic with total spin $s_G =N(s_1 - s_2)$. We find that there is a gapless excitation to a state with spin $s_G -1$, and a gapped excitation to a state with spin $s_G +1$. Surprisingly, the correlation length in the ground state is found to be very small for this gapless system. The DMRG analysis shows that the chain is susceptible to a conditional spin-Peierls instability. Furthermore, our studies of the magnetization, magnetic susceptibility $\chi$ and specific heat show strong magnetic-field dependences. The product $\chi T$ shows a minimum as a function of temperature T at low magnetic fields; the minimum vanishes at high magnetic fields. This low-field behavior is in agreement with earlier experimental observations. The specific heat shows a maximum as a function of temperature, and the height of the maximum increases sharply at high magnetic fields. Although all the three systems show qualitatively similar behavior, there are some notable quantitative differences between the systems in which the site spin difference, $|s_1 - s_2|$, is large and small respectively.Comment: 16 LaTeX pages, 13 postscript figure

Inorganic carbon concentrating mechanisms in free-living and symbiotic dinoflagellates and chromerids

Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms

Flat-Band Ferromagnetism in Organic Polymers Designed by a Computer Simulation

By coupling a first-principles, spin-density functional calculation with an exact diagonalization study of the Hubbard model, we have searched over various functional groups for the best case for the flat-band ferromagnetism proposed by R. Arita et al. [Phys. Rev. Lett. {\bf 88}, 127202 (2002)] in organic polymers of five-membered rings. The original proposal (poly-aminotriazole) has turned out to be the best case among the materials examined, where the reason why this is so is identified here. We have also found that the ferromagnetism, originally proposed for the half-filled flat band, is stable even when the band filling is varied away from the half-filling. All these make the ferromagnetism proposed here more experimentally inviting.Comment: 11 pages, 13figure