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Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments
(Oxford University Press, 2017)
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different ...
Measurement of work in single-molecule pulling experiments
(AIP Publishing, 2009)
A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify ...
Counter-propagating dual-trap optical tweezers based on linear momentum conservation
(AIP Publishing, 2013)
We present a dual-trap optical tweezers setup which directly measures forces using linear momentum conservation. The setup uses a counter-propagating geometry, which allows momentum measurement on each ...
Single-molecule derivation of salt dependent base-pair free energies in DNA
(National Academy of Sciences, 2010)
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in ...
Improving signal/noise resolution in single-molecule experiments using molecular constructs with short handles
(Elsevier, 2011)
We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness ...
Dynamic force spectroscopy of DNA hairpins: II. Irreversibility and dissipation
(IOP Publishing, 2009)
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 ...
Dynamic force spectroscopy of DNA hairpins: I. Force kinetics and free energy landscapes
(IOP Publishing, 2009)
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive ...
Work distributions in the T = 0 random field Ising model
(American Physical Society, 2008)
We perform a numerical study of the three-dimensional random-field Ising model at T= 0. We compare work distributions along metastable trajectories obtained with the single-spin flip dynamics with the ...
Investigating the thermodynamics of small biosystems with optical tweezers
(Elsevier, 2010)
We present two examples of how single-molecule experimental techniques applied to biological systems can give insight into problems within the scope of equilibrium and nonequilibrium mesoscopic ...
Single-molecule stochastic resonance
(American Physical Society, 2012)
Stochastic resonance (SR) is a well-known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic (random or probabilistic) ...