Papers by Tobias Ambjornsson
Physical Review E, 2003
We investigate the drift velocity v(drift) of ellipsoidal polarizable particles (ellipsoids and c... more We investigate the drift velocity v(drift) of ellipsoidal polarizable particles (ellipsoids and coated ellipsoids), driven through a viscous fluid by an electric or electromagnetic field intensity gradient. At low Reynolds number and in the dipole approximation v(drift) is proportional to the square of the principal axis along the direction of motion multiplied by a form factor, which is weakly depending on the shape of the particle, and by a frequency and shape dependent factor f(omega). Near frequencies where the real part of epsilon (m)f(omega) changes sign ( epsilon (m) is the relative dielectric function of the medium in which the partcle is immersed), v(drift) is sensitive to the shape of the particle. We suggest that our results can be used for the experimental separation of neutral polarizable particles with respect to size or shape.
Physical Review E, 2005
We study the size fluctuations of a local denaturation zone in a DNA molecule, in the presence of... more We study the size fluctuations of a local denaturation zone in a DNA molecule, in the presence of proteins that exclusively bind to single-stranded DNA, based on a (2 + 1)-dimensional master equation governing the time evolution of the probability distribution P (m, n, t) to find a bubble of size m with n bound proteins. In particular, by tuning the physical parameters we can drive the system from undisturbed bubble fluctuations to full, binding protein-induced denaturation. Moreover, we determine the effective free energy landscape of the DNA-bubble and its lifetime. 87.14.Gg Under physiological conditions, the Watson-Crick double-helix is the thermodynamically stable configuration of a DNA molecule. This stability is effected by the specific Watson-Crick H-bonding, whose key-lock principle guarantees the high level of fidelity during replication and transcription; and by the stronger base-stacking between neighboring base-pairs causing hydrophobic interactions between the planar aromatic bases .
Physical Review Letters, 2006
We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a m... more We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a biological sequence of the T7 bacteriophage. Quantitative agreement with data from fluorescence correlation spectroscopy (FCS) is demonstrated.
Biophysical Journal, 2007
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA... more While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiation and DNA's interaction with selectively single-stranded DNA binding proteins. Motivated by this, we consider the bubble breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master equation and complementary stochastic Gillespie simulations, providing the bubble size and the position of the bubble along the sequence as a function of time. We utilize new experimental data that independently obtain stacking and hydrogen bonding contributions to DNA stability. We calculate the spectrum of relaxation times and the experimentally measurable autocorrelation function of a fluorophore-quencher tagged base-pair, and demonstrate good agreement with fluorescence correlation experiments. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a promoter sequence of the T7 phage. The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.
Physical Review Letters, 2005
We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of pa... more We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of particles (`proteins'), whose search combines 1D diffusion along the chain, Levy type diffusion mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search.
Chemical Physics, 2008
We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore... more We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two-particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial particle positions and all times. The two-particle PDF is used to obtain the tagged particle PDF. For the general N-particle case (N large) we perform stochastic simulations using our new computationally efficient stochastic simulation technique based on the Gillespie algorithm. We find that the mean square displacement for a tagged particle scales as the square root of time (as for identical particles) for long times, with a prefactor which depends on the diffusion constants for the particles; these results are in excellent agreement with very recent analytic predictions in the mathematics literature.
Physical Biology, 2004
We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the pres... more We investigate the translocation of a stiff polymer through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind reversibly to the polymer on both sides of the membrane. A bound chaperone covers one (univalent binding) or many (multivalent binding) binding sites. Assuming that the diffusion of the chaperones is fast compared to the rate of translocation we describe the process by a one-dimensional master equation. We expand previous models by a detailed study of the effective force in the master equation, which is obtained by the appropriate statistical mechanical average over the chaperone states. The dependence of the force on the degree of valency (the number of binding sites occupied by a chaperone) is studied in detail. We obtain finite size corrections (to the thermodynamical expression for the force), which, for univalent binding, can be expressed analytically. We finally investigate the mean velocity for translocation as a function of chaperone binding strength and size. For both univalent and multivalent binding simple results are obtained for the case of a sufficiently long translocating polymer.
Physical Review E, 2004
We derive an expression for the polarizability of an ellipsoidally shaped cell-like structure at ... more We derive an expression for the polarizability of an ellipsoidally shaped cell-like structure at field frequencies where membrane molecular resonances ͑vibrational and electronic͒ are important. We first present analytical results for the dielectric function of a flat, dipole coupled, bilayer consisting of molecules with one prominent resonance frequency. Due to the nature of the dipole coupling the dielectric function is different for the field being parallel or perpendicular to the bilayer normal with two new resonance frequencies ϭ 0ʈ and ϭ 0Ќ . We then combine this anisotropic bilayer dielectric function with the analytical solution of Gauss equation for an ellipsoid with an anisotropic coating ͑the coating dielectric function being different parallel and perpendicular to the coating normal͒ in order to find the polarizability of an ellipsoidal bilayer membrane. In particular, we find that for a thin-walled ͑compared to the size of the cell͒ membrane the resonance frequencies of the polarizability are the same as for a flat bilayer ͑independent of the cell shape͒. However, our analytic result for the geometric weights for the oscillator strengths is sensitive to the shape; the geometric weight for the ϭ 0Ќ (ϭ 0ʈ ) peak is largest when the external field is along the largest ͑smallest͒ axis. The geometric weights are shown to be constrained by three sum rules.
Journal of Physics-condensed Matter, 2009
While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range... more While the Watson-Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland-Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins.
We present an analytic theory for the optical properties of ellipsoidal plasmonic particles cover... more We present an analytic theory for the optical properties of ellipsoidal plasmonic particles covered by anisotropic molecular layers. The theory is applied to the case of a prolate spheroid covered by chromophores oriented parallel and perpendicular to the metal surface. For the case that the molecular layer resonance frequency is close to being degenerate with one of the particle plasmon resonances strong hybridization between the two resonances occur. Approximate analytic expressions for the hybridized resonance frequencies, their extinction cross section peak heights and widths are derived. The strength of the molecular -plasmon interaction is found to be strongly dependent on molecular orientation and suggest that this sensitivity could be the basis for novel nanoparticle based bio/chemo-sensing applications.
Chemical Physics, 2002
We study the process of charged polymer translocation, driven by an external electric potential, ... more We study the process of charged polymer translocation, driven by an external electric potential, through a narrow pore in a membrane. We assume that the number of polymer segments, m, having passed the entrance pore mouth, is a slow variable governing the translocation process. Outside the pore the probability that there is an end segment at the entrance pore mouth, is taken as the relevant parameter. In particular we derive an expression for the free energy as a function of m, F(m). F(m) is used in the Smoluchowski equation in order to obtain the flux of polymers through the pore. In the low voltage regime we find a thresholdlike behavior and exponential dependence on voltage. Above this regime the flux depends linearly on the applied voltage. At very high voltages the process is diffusion limited and the flux saturates to a constant value. The model accounts for all features of the recent experiments by Henrickson [et al.] [Phys. Rev. Lett. 85, 3057 (2000)] for the flux of DNA molecules through an alpha-hemolysin pore as a function of applied voltage.
Physical Review E, 2007
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the d... more After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent single-stranded bubbles. Their unzipping and zipping dynamics can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.
Physical Review E, 2007
We investigate the effect on biomembrane mechanical properties due to the presence an external po... more We investigate the effect on biomembrane mechanical properties due to the presence an external potential for a non-conductive non-compressible membrane surrounded by different electrolytes. By solving the Debye-Huckel and Laplace equations for the electrostatic potential and using the relevant stress-tensor we find: in (1.) the small screening length limit, where the Debye screening length is smaller than the distance between the electrodes, the screening certifies that all electrostatic interactions are short-range and the major effect of the applied potential is to decrease the membrane tension and increase the bending rigidity; explicit expressions for electrostatic contribution to the tension and bending rigidity are derived as a function of the applied potential, the Debye screening lengths and the dielectric constants of the membrane and the solvents. For sufficiently large voltages the negative contribution to the tension is expected to cause a membrane stretching instability. For (2.) the dielectric limit, i.e. no salt (and small wavevectors compared to the distance between the electrodes), when the dielectric constant on the two sides are different the applied potential induces an effective (unscreened) membrane charge density, whose long-range interaction is expected to lead to a membrane undulation instability.
Based on modern single molecule techniques, we devise a number of possible experimental setups to... more Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out about the solvent conditions such as ionic strength, presence of binding proteins, etc. By measuring dynamical quantities in particular, rather sensitive nanoprobes may be constructed with contemporary instruments.
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Papers by Tobias Ambjornsson