Bulletin of the American Physical Society
APS March Meeting 2010
Volume 55, Number 2
Monday–Friday, March 15–19, 2010; Portland, Oregon
Session B10: Focus Session: Single Molecule Biophysics and Chemical Physics II |
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Sponsoring Units: DCP DBP DPOLY Chair: Antoine Van Oijen, Harvard Medical School Room: A106 |
Monday, March 15, 2010 11:15AM - 11:51AM |
B10.00001: Using Transcription to Measure DNA Mechanics One Molecule at a Time Invited Speaker: There is a rich and interesting interplay between the informational and physical characteristics of genomes. Examples range from how DNA is packed in organisms as diverse as bacteriophage and humans to the biophysical factors dictating nucleosome accessibility to the nature of DNA looping as part of the transcriptional repertoire of a host of different cells. In this talk I will describe recent experiments that explore the mechanics of genome management, how simple models can be constructed to interpret such experiments (and used to make predictions for new experiments) and examples of both single-molecule and single-cell approaches to the study of how cells make decisions and the way in which DNA mechanics governs these decisions. Special attention will be given to using Lac repressor as a tool for reading out the flexibility of different DNA sequences. [Preview Abstract] |
Monday, March 15, 2010 11:51AM - 12:03PM |
B10.00002: Molecular origins of DNA flexibility: Sequence effects on conformational and mechanical properties Vanessa Ortiz, Juan J. de Pablo The bendedness (kinks) and bendability (flexibility) of DNA are believed to play a major role in the affinity of certain sequences for histone binding. Theoretical and experimental attempts to observe and quantify bendedness and bendability have been hindered by an inability to directly resolve DNA structure and dynamics at the base-pair level. We have developed a model of DNA that includes previously unavailable features that are crucial for understanding bendedness and bendability at the molecular and microscopic length-scales. These include hybridization, sequence-dependent deformability and electrostatic effects. The model reveals that sequence does influence bendedness through the creation of kinks that arise when certain motifs slide past others to form non-native contacts. Bendability is shown to be anisotropic, with a directionality that is encoded by sequence. These observations are shown to help explain the biologically observed preference of certain DNA sequences for histone binding. [Preview Abstract] |
Monday, March 15, 2010 12:03PM - 12:15PM |
B10.00003: Intrinsic and force-generated cooperativity in a theory of DNA bending proteins Houyin Zhang, John F. Marko We study a statistical-mechanical model of the binding of DNA-bending proteins to the double helix including applied tension and binding cooperativity effects. We find that intrinsic cooperativity of binding sharpens force-extension curves, and causes enhancement of fluctuation of extension and protein occupation. This model also allows us to estimate the intrinsic cooperativity in experiments by measuring the peak value of the slope of extension vs. chemical potential curves. In addition, we find clear signatures of cooperativity in the mechanical signals even in the absence of explicit intrinsic (energetic) cooperativity. To further understand this effect, we analyze a model with a pair of bends at variable spacing and derive a spacing-dependent free energy of interaction between the two proteins. We find that the interaction, in a model without helical phasing, is always attractive, and has an exponential decay as a function of bend spacing. We also find that for forces greater than $k_BT/A$, where $A$ is the persistence length, the interaction correlation length varies as $\sqrt{k_BTA/(4f)}$, and the interaction strength varies approximately linearly with force until the proteins are forced to unbend. Our results apply to single molecule experiments on DNA-bending proteins and also suggest mechanisms for control of the distribution of proteins bound along DNA in vivo. [Preview Abstract] |
Monday, March 15, 2010 12:15PM - 12:27PM |
B10.00004: Interplay between elasticity and binding in DNA-protein complexes Yitzhak Rabin, Shay Rappaport We present a model of non-specific cooperative binding of proteins to DNA in which the binding of isolated proteins generates local bends but binding of proteins at neighboring sites on DNA straightens the polymer. We solve the statistical mechanical problem and calculate the effective persistence length, site occupancy and cooperativity. Cooperativity leads to non-monotonic variation of the persistence length with protein concentration, in qualitative agreement with recent single molecule experiments on HU-DNA complexes. Elastic effects on adsorption of proteins (a bent chain has a higher entropy!) lead to unusual shape of the binding isotherm. [Preview Abstract] |
Monday, March 15, 2010 12:27PM - 12:39PM |
B10.00005: Development of dumbbell model for the electrophoresis of end-labeled DNA Henry Lau, Lynden Archer The electrophoretic behavior of end-labeled DNA in free solution is investigated. This talk focuses on using a simple dumbbell model for the labeled DNA to study the effect of the applied field, label size, and chain stiffness on DNA conformation and electrophoretic mobility. Experimental results obtained via capillary electrophoresis are in general agreement with predictions. Extending our model to study high field dynamic behavior, a scaling approach is employed to account for the field-induced alignment of chain segments at progressively higher applied fields. We discuss our results in the context of optimizing the size-based separation of DNA. [Preview Abstract] |
Monday, March 15, 2010 12:39PM - 12:51PM |
B10.00006: Molecular Dynamics Simulations of the Transport of Single DNA Nucleotides Through Nanochannels Brian Novak, Dorel Moldovan, Dimitris Nikitopoulos, Steven Soper Transport of single molecules through nano-confined geometries can be used to identify them via their unique flight times. The movement of the nucleotides in aqueous solution flowing through nanochannels was studied using nonequilibrium molecular dynamics simulations. Initial 150 ns simulations of nucleotides in 89 mM NaCl solution in 3.0 nm slits with walls composed of disordered carbon atoms show well separated flight times for the nucleotides C and T. The fluid was driven by gravity-like forces to an average velocity of about 1.0 m/s. In contrast, the flight times for A and G are within one standard deviation of each other and the differences between A and T and between G and C are roughly two standard deviations. Our simulations show that the nucleotides are adsorbed and desorbed from the wall multiple times while moving along the channel. The evidence shows that the hydrophobicity of T is responsible for its longer residence times in contact with the also hydrophobic wall and longer flight time relative to C. [Preview Abstract] |
Monday, March 15, 2010 12:51PM - 1:03PM |
B10.00007: The scaling laws for polymer translocation through a nanopore depend on pore width Gary W. Slater, Hendrick W. de Haan Results from an extensive Langevin Dynamics simulation study mapping the scaling of the translocation time with polymer length $\tau \sim $N$^{\alpha }$ over a wide range of nanopore widths will be presented. It is found that the scaling exponent $\alpha $ varies from 2.2 for a tight-pore up to an apparent saturation value of about 3.0 for wide pores. Further characterization given by measuring the average number of monomers in the pore $\langle $n$_{p}\rangle $ reveals not only pore-size dependence, but also that $\langle $n$_{p}\rangle $ \textit{decreases} with increasing N but increases as translocation proceeds. These results may explain why different simulation methods appear to predict different values for $\alpha$. [Preview Abstract] |
Monday, March 15, 2010 1:03PM - 1:15PM |
B10.00008: Dynamics of polymer translocation rectified by attractive binding particles Aniket Bhattacharya, Christopher Lorscher, Tapio Ala-Nissila, Wokyung Sung We study translocation of flexible homopolymer chains through a nanopore in presence of attractive particles those bind reversibly on the $trans$ part of the chain and responsible for successful translocation using Langevin dynamics simulation. We study the mean first passage time (MFPT) as a function of the density $\rho_{att}$ and strength $\epsilon_{att}$ of the attractive particles respectively and find that it is qualitatively different compared to the results obtained for straight(rigid) chains$^1$. Further, we find the average translocation time $\langle \tau \rangle \sim N^{1.5}$ which is faster than the lower bound predicted by simple one dimensional Langevin equation. Finally, we find that for certain combination of $\rho_{att}$ and $\epsilon_{att}$ the translocation is most efficient. We interpret it as a resonant assisted activated translocation. We discuss relevance of our studies in biological translocation processes.\\ $^1$R. Zandi, D. Reguera, J. Rudnick and W.~M. Gelbart, Proc. Natl. Acad. Sci. USA {\bf 100} 8649 (2003).\\ $^2$W. Sung and P.~J. Park, Phys. Rev. Lett. {\bf 77}, 783 (1996). [Preview Abstract] |
Monday, March 15, 2010 1:15PM - 1:27PM |
B10.00009: Rectified polymer translocation induced by solvent assymetry between $cis$ and $trans$ compartments Christopher Lorscher, Aniket Bhattacharya, Tapio Ala-Nissila We report Langevin dynamics simulation studies of translocation of a homopolymer through a nano pore driven by different solvent conditions at either side of the pore. The solvent at the $cis$ compartment is modeled as a ``\textit{good solvent}'' while the solvent at the $trans$ side is modeled as a ``\textit{bad solvent}'' so that the translocated beads of the polymer conforms to a globule and inhibits back translocation from the $trans$ to the $cis$ side. Therefore, the translocating polymer acts like a \textit{Brownian Ratchet}. We study the translocation as a function of the dimensionless quantity $\epsilon/k_BT$, where $\epsilon$ is the strength of the attractive interaction at the $cis$ side, $k_B$ is the Boltzmann constant, and $T$ is the temperature respectively for several chain length $N$. We find that as $N$ gets larger the mean translocation time $\langle \tau \rangle \sim N$ and shows a rather weak dependence on the parameter $\epsilon/k_BT$ . This is consistent with the observation that excepting for the last few monomers, the velocity of the individual monomer s $v(m)$ is roughly constant being independent of the monomer index $m$. We further discuss a plausible physical picture leading to such chain length dependence. [Preview Abstract] |
Monday, March 15, 2010 1:27PM - 1:39PM |
B10.00010: Stretching weakly bending filaments with spontaneous curvature in two dimensions Panayotis Benetatos, Eugene Terentjev Some important biomolecules are known to posses spontaneous (intrinsic) curvature. Using a simple extension of the wormlike chain model, we study the response of a weakly bending filament in two dimensions to a pulling force applied at its ends. The spontaneous curvature of such a chain or filament can in general be arc-length dependent and we study a case of sinusoidal variation, from which an arbitrary case can be reconstructed via Fourier transformation. We obtain analytic results for the force-extension relationship and the width of transverse fluctuations. We show that spontaneous-curvature undulations can affect the force-extension behavior even in relatively flexible filaments with a persistence length smaller than the contour length. [Preview Abstract] |
Monday, March 15, 2010 1:39PM - 1:51PM |
B10.00011: Solvable model of mechanical unfolding of biopolymers Donald Jacobs, Dennis Livesay, Oleg Vorov We present exact analytical results for a hairpin to coil transition induced through mechanical pulling of dsDNA or peptides (beta-hairpin) within a distance constraint model [1], taking into account geometry of conformations. Starting from ab initio considerations, the configuration partition function is calculated exactly. Among other thermodynamic response functions, an expression for the end-to-end extension as a function of the applied force at a given temperature is derived. Our theoretical results agree well with data from single-molecule stretching experiments [2]. The employed method is general, and promises to remain a tractable computational approach when applied to larger, more complicated macromolecules. This work is supported by NIH R01 GM073082.\\[4pt] [1] O.K. Vorov, D.R. Livesay and D.J. Jacobs, ENTROPY, v.10 (3) 285-308 (2008).\\[0pt] [2] O.K. Vorov, D.R. Livesay and D.J. Jacobs, to be subm. to Phys. Rev. Lett., in preparation. [Preview Abstract] |
Monday, March 15, 2010 1:51PM - 2:03PM |
B10.00012: Inherent Tension in Chemical Bonds James Brock, Qi Liao, Michael Rubinstein A method is provided for relating average internal tension in bonds between atoms or monomeric units to the external tension applied to them using computer simulations. In dimensions greater than one, there is an average internal tension in bonds on the order of 100 pN even in the absence of an externally applied tension. This non-zero average internal tension is due to asymmetry of thermal fluctuations of bond length and increases with increasing dimensionality. Results from molecular dynamics simulations are in perfect agreement with analytical calculations of tension. [Preview Abstract] |
Monday, March 15, 2010 2:03PM - 2:15PM |
B10.00013: Information theory resolution limits and hidden Markov model analysis of single molecule fluorescence David Talaga Time correlated single photon counting determines luminescence lifetime information on a single molecule level. This paper develops a formalism to allow information-theory analysis of the ability of luminescence lifetime measurements to resolve states in a single molecule. It analyzes experimental losses of information due to instrument response, digitization, and background. This paper shows how to use the information theoretical formalism to evaluate the number of photons required to distinguish dyes that differ only by lifetime, by electron transfer quenching, or by FRET. It shows how the differences between the lifetime of signal and background can help distinguish the dye position in an excitation beam. Many systems follow phenomenological kinetics where discrete states are connected by rate equations. However systems with low energetic barriers and multiple interchanging structures are not as amenable to this approach. Such continuous state spaces are best described by Langevin dynamics (LD) and an appropriate Fokker-Planck equation (FPE). This paper develops hidden Markov models (HMMs) for LD and the FPE. It shows how molecular friction and activation barrier along an effective coordinate can be estimated. It utilizes the models to guide the design of single molecule experiments. [Preview Abstract] |
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