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Search Publications by

Paul Patrone (Fed)

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Displaying 1 - 25 of 33

Optofluidic Flow Meter for sub-nanoliter per minute flow measurements

January 31, 2022
Jalal Sadeghi, Paul Patrone, Anthony J. Kearsley, Gregory A. Cooksey
Performance improvements in microfluidic systems depend on accurate measurement and control of fluids on the micro- and nanoscale, and new applications are continuously moving the needle to lower volumetric flow rates. This work focuses on improving an

Failure mechanisms in DNA self-assembly: Barriers to single fold yield

February 23, 2021
Jacob Majikes, Paul Patrone, Anthony J. Kearsley, Michael P. Zwolak, James Liddle
Understanding the folding process of DNA origami is a critical steppingstone to the broader implementation of nucleic acid nanofabrication technology but is notably non-trivial. Origami are formed by several hundred cooperative hybridization events – folds

Matching and comparing objects in a serial cytometer

October 4, 2020
Nikita Podobedov, Matthew DiSalvo, Jason A. Hsu, Paul Patrone, Gregory A. Cooksey
Flow cytometers are indispensable for clinical studies, yet are hindered by inherent uncertainties. We have developed an optofluidic device capable of multiple measurements along a microfluidic channel, whereby many of the uncertainty components can be

Serial microfluidic cytometry with inertial and hydrodynamic flow focusing

October 4, 2020
Matthew DiSalvo, Paul Patrone, Gregory A. Cooksey
Microfluidics are increasingly used to develop flow cytometers with novel functionalities. Although various approaches exist to control particle positioning within microfluidics, the magnitude and mechanisms of measurement uncertainties that arise from


October 3, 2020
Gregory A. Cooksey, Paul Patrone, James R. Hands, Stephen E. Meek, Anthony J. Kearsley
This work describes a new method for continuous measurement of flow in a microchannel from 1 nL/min to 1000 nL/min using an optofluidic device with waveguides that deliver and collect light from small regions of a microfluidic channel. By relating the

Measuring Microfluidic Flow Rates: Monotonicity, Convexity and Uncertainty

August 20, 2020
Paul Patrone, Qing Hai Li, Gregory A. Cooksey, Anthony J. Kearsley
A class of non-linear integro-differential equations characterizing microfluidic measurements is considered. Under reasonable conditions, these non-linear integro-differential equations admit solutions that are convex functions of an interesting flow-rate

Revealing thermodynamics of DNA origami folding via affine transformations

June 4, 2020
Jacob M. Majikes, Paul N. Patrone, Daniel R. Schiffels, Michael P. Zwolak, Anthony J. Kearsley, Samuel P. Forry, James A. Liddle
Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative

Best Practices for Quantification of Uncertainty and Sampling Quality in Molecular Simulations

October 27, 2018
Alan Grossfield, Paul Patrone, Daniel R. Roe, Andrew J. Schultz, Daniel Siderius, Daniel M. Zuckerman
The quantitative assessment of uncertainty and sampling quality is essential in molecular simulation. Many systems of interest are highly complex, often at the edge of current computational capabilities. Modelers must therefore analyze and communicate

Bayesian Calibration of Transferable, Coarse-Grained Force Fields

April 15, 2016
Thomas W. Rosch, Frederick R. Phelan Jr., Paul Patrone
Generating and calibrating forces that are transferable across a range of state-points remains a challenging problem in coarse-grained (CG) molecular dynamics (MD). In this work, we present a Bayesian correction algorithm, inspired by ideas from

Kilohertz Rotation of Nanorods Propelled by Ultrasound, Traced by Microvortex Advection of Nanoparticles

August 26, 2014
Andrew L. Balk, Lamar O. Mair, Pramod Mathai, Paul N. Patrone, Wei Wang, Suzanne Ahmed, Thomas Mallouk, James A. Liddle, Samuel M. Stavis
We measure the microvortical flows around gold nanorods propelled by ultrasound in water using polystyrene nanoparticles as optical tracers. We infer the rotational frequencies of such nanomotors assuming a hydrodynamic model of this interaction. In this

High-speed, high-purity separation of gold nanoparticle-DNA origami constructs using centrifugation

July 23, 2014
Seung H. Ko, Luis F. Vargas Lara, Paul Patrone, Samuel Stavis, Francis W. Starr, Jack F. Douglas, James Alexander Liddle
DNA origami is a powerful platform for assembling gold nanoparticle constructs, an important class of nanostructure with numerous applications. Such constructs are assembled by the association of complementary DNA oligomers. These association reactions