相关论文: Splitting probabilities as a test of reaction coor…
We suggest simple and useful method to extract breakup probabilities from the experimental elastic backscattering probabilities in the reactions with toughly and weakly bound nuclei.
We have measured the velocity of a running crack in brittle single crystal silicon as a function of energy flow to the crack tip. The experiments are designed to permit direct comparison with molecular dynamics simulations; therefore the…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
Reaction coordinates are widely used throughout chemical physics to model and understand complex chemical transformations. We introduce a definition of the natural reaction coordinate, suitable for condensed phase and biomolecular systems,…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the…
Splitting probabilities quantify the likelihood of a given outcome out of competitive events. This key observable of random walk theory, historically introduced as the gambler's ruin problem, is well understood for memoryless (Markovian)…
The mechanical stretching of single poly-proteins is an emerging tool for the study of protein (un)folding, chemical catalysis and polymer physics at the single molecule level. The observed processes i.e unfolding or reduction events, are…
We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
For diffusive stochastic dynamics, the probability to observe any individual trajectory is vanishingly small, making it unclear how to experimentally validate theoretical results for ratios of path probabilities. We provide the missing link…
Single-molecule force spectroscopy has proven to be a powerful tool for studying the kinetic behavior of biomolecules. Through application of an external force, conformational states with small or transient populations can be stabilized,…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Bell-type experiments that test correlated observables typically involve measurements of spin or polarization on multi-particle systems in singlet states. These observables are all non-commuting and satisfy an uncertainty relation.…
A mixture with varying concentrations is a modification of a finite mixture model in which the mixing probabilities (concentrations of mixture components) may be different for different observations. In the paper, we assume that the…
The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently,…
Many biomolecules have flexible structures, requiring distributional estimates of their conformations. Experiments to acquire distributional data typically measure pairs of labels separately, losing information on the joint distribution.…