Velocity and processivity of helicase unwinding of double-stranded nucleic acids

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single-stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations to open dsNA base pairs before it can advance and inhibit NA closing. An active helicase directly destabilizes dsNA base pairs, accelerating the opening rate. Here we extend this model to include helicase unbinding from the nucleic-acid strand. The helicase processivity depends on the form of the interaction potential. A passive helicase has a mean attachment time which does not change between ss translocation and ds unwinding, while an active helicase in general shows a decrease in attachment time during unwinding relative to ss translocation. In addition, we describe how helicase unwinding velocity and processivity vary if the base-pair binding free energy is changed.Comment: To appear in special issue on molecular motors, Journal of Physics - Condensed Matte

Controlled Irradiative Formation of Penitentes

Spike-shaped structures are produced by light-driven ablation in very different contexts. Penitentes 1-4 m high are common on Andean glaciers, where their formation changes glacier dynamics and hydrology. Laser ablation can produce cones 10-100 microns high with a variety of proposed applications in materials science. We report the first laboratory generation of centimeter-scale snow and ice penitentes. Systematically varying conditions allows identification of the essential parameters controlling the formation of ablation structures. We demonstrate that penitente initiation and coarsening requires cold temperatures, so that ablation leads to sublimation rather than melting. Once penitentes have formed, further growth of height can occur by melting. The penitentes intially appear as small structures (3 mm high) and grow by coarsening to 1-5 cm high. Our results are an important step towards understanding and controlling ablation morphologies.Comment: Accepted for publication in Physical Review Letter

Formation of Structure in Snowfields: Penitentes, Suncups, and Dirt Cones

Penitentes and suncups are structures formed as snow melts, typically high in the mountains. When the snow is dirty, dirt cones and other structures can form instead. Building on previous field observations and experiments, this work presents a theory of ablation morphologies, and the role of surface dirt in determining the structures formed. The glaciological literature indicates that sunlight, heating from air, and dirt all play a role in the formation of structure on an ablating snow surface. The present work formulates a mathematical model for the formation of ablation morphologies as a function of measurable parameters. The dependence of ablation morphologies on weather conditions and initial dirt thickness are studied, focusing on the initial growth of perturbations away from a flat surface. We derive a single-parameter expression for the melting rate as a function of dirt thickness, which agrees well with a set of measurements by Driedger. An interesting result is the prediction of a dirt-induced travelling instability for a range of parameters.Comment: 28 pages, 13 figure

Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport

Unlike equilibrium statistical mechanics, with its well-established foundations, a similar widely-accepted framework for non-equilibrium statistical mechanics (NESM) remains elusive. Here, we review some of the many recent activities on NESM, focusing on some of the fundamental issues and general aspects. Using the language of stochastic Markov processes, we emphasize general properties of the evolution of configurational probabilities, as described by master equations. Of particular interest are systems in which the dynamics violate detailed balance, since such systems serve to model a wide variety of phenomena in nature. We next review two distinct approaches for investigating such problems. One approach focuses on models sufficiently simple to allow us to find exact, analytic, non-trivial results. We provide detailed mathematical analyses of a one-dimensional continuous-time lattice gas, the totally asymmetric exclusion process (TASEP). It is regarded as a paradigmatic model for NESM, much like the role the Ising model played for equilibrium statistical mechanics. It is also the starting point for the second approach, which attempts to include more realistic ingredients in order to be more applicable to systems in nature. Restricting ourselves to the area of biophysics and cellular biology, we review a number of models that are relevant for transport phenomena. Successes and limitations of these simple models are also highlighted.Comment: 72 pages, 18 figures, Accepted to: Reports on Progress in Physic