arXiv subjects

Juan G. Santiago

Publications and source records attributed to Juan G. Santiago.

11 recordsLinked to original sources

arXiv2024

Vertex pinning and stretching of single molecule DNA in a linear polymer solution

Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA molecules in a neutral linear polymer solution were driven with an axial electric field through microchannels and their dynamics were studied using fluorescence microscopy. We observed that above a threshold electric field, individual DNA molecules become pinned to the channel walls at a vertex on each molecule and are stretched in the direction opposite to the electric field. Upon removal of the electric field, pinned DNA molecules undergo relaxation within a few seconds to a Brownian coil around the vertex. After 10s of seconds, DNA is released and free to electromigrate. The method enables high quality imaging of single-molecule DNA with high throughput using simple-to-fabricate fluidic structures. We analyze the conditions needed for trapping, relaxation dynamics, and the repeatability of vertex pinning. We hypothesize DNA entangles with neutral linear polymers adsorbed to walls. We hypothesize that a sufficiently high electric force on the DNA is required to expel a hydration layer between the DNA and the wall-adsorbed neutral linear polymers. The elimination of the hydration layer may increase the friction between charged DNA and the uncharged polymer, promoting vertex pinning of DNA.

cond-mat.soft↗

arXiv2023

Taylor dispersion in arbitrarily shaped axisymmetric channels

Advective dispersion of solutes in long thin axisymmetric channels is important to the analysis and design of a wide range of devices, including chemical separation systems and microfluidic chips. Despite extensive analysis of Taylor dispersion in various scenarios, most studies focused on long-term dispersion behavior and cannot capture the transient evolution of solute zone across the spatial variations in the channel. In the current study, we analyze the Taylor-Aris dispersion for arbitrarily shaped axisymmetric channels. We derive an expression for solute dynamics in terms of two coupled ordinary differential equations (ODEs). These two ODEs allow prediction of the time evolution of the mean location and axial (standard deviation) width of the solute zone as a function of the channel geometry. We compare and benchmark our predictions with Brownian dynamics simulations for a variety of cases including linearly expanding/converging channels and periodic channels. We also present an analytical description of the physical regimes of transient positive versus negative axial growth of solute width. Finally, to further demonstrate the utility of the analysis, we demonstrate a method to engineer channel geometries to achieve desired solute width distributions over space and time. We apply the latter analysis to generate a geometry that results in a constant axial width and a second geometry that results in a sinusoidal axial variance in space.

physics.flu-dyn↗

arXiv2022

Microfluidic Isotachophoresis: Theory and Applications

Isotachophoresis (ITP) is a versatile electrophoretic technique which can be used for sample preconcentration, separation, purification, mixing, and control and acceleration of chemical reactions. Although the basic technique is nearly a century old and widely used, there has been a persistent need for an easily approachable, succinct, and rigorous review of ITP theory and analysis. This is important as interest and adoption of the technique has grown over the last two decades, especially because of its implementation into microfluidics and integration with on-chip chemical and biochemical assays. We here provide a review of ITP theory with a strong emphasis on steady and unsteady transport starting from physicochemical first principles including conservation of species, conservation of current, the approximation of charge neutrality, pH equilibrium of weak electrolytes, and so-called regulating functions governing transport dynamics. We combine these generally applicable (to all types of ITP) theoretical discussions with applications of ITP in the field of microfluidic systems, particularly on-chip biochemical analyses. Our discussion includes principles governing ITP focusing of weak and strong electrolytes, ITP dynamics in peak and plateau modes, review of simulation tools, experimental tools and detection methods, applications of ITP for on-chip separations and trace analyte manipulation, and design considerations and challenges for microfluidic ITP systems. We conclude with remarks on possible future research directions. The intent of this review is to help make ITP analysis and design principles more accessible to the scientific and engineering communities, and to provide a rigorous basis for increased adoption of ITP into microfluidics.

physics.chem-ph↗

arXiv2022

Liquid Heterostructures: Generation of Liquid-Liquid Interfaces in Free-Flowing Liquid Sheets

Chemical reactions and biological processes are often governed by the structure and transport dynamics of the interface between two liquid phases. Despite their importance, our microscopic understanding of liquid-liquid interfaces has been severely hindered by difficulty in accessing the interface through the bulk liquid. Here we demonstrate a method for generating large-area liquid-liquid interfaces within free-flowing liquid sheets, which we call liquid heterostructures. These sheets can be made thin enough to transmit photons from across the spectrum, which also minimizes the amount of bulk liquid relative to the interface and makes them ideal targets for a wide range of spectroscopies and scattering experiments. The sheets are produced with a microfluidic nozzle that impinges two converging jets of one liquid onto two sides of a third jet of another liquid. The hydrodynamic forces provided by the colliding jets both produce a multilayered laminar liquid sheet with the central jet is flattened in the middle. Infrared microscopy, white light reflectivity, and imaging ellipsometry measurements demonstrate that the buried layer has a tunable thickness and displays well-defined liquid-liquid interfaces, and that the inner layer can be thinner than 100 nm.

physics.chem-ph↗

arXiv2018

Performance Metrics for the Objective Assessment of Capacitive Deionization Systems

In the growing field of capacitive deionization (CDI), a number of performance metrics have emerged to describe the desalination process. Unfortunately, the separation conditions under which these metrics are measured are often not specified, resulting in optimal performance at minimal removal. Here we outline a system of performance metrics and reporting conditions that resolves this issue. Our proposed system is based on volumetric energy consumption (Wh/m$^3$) and throughput productivity (L/h/m$^2$) reported for a specific average concentration reduction, water recovery, and feed salinity. To facilitate and rationalize comparisons between devices, materials, and operation modes, we propose a nominal standard testing condition of removing 5 mM from a 20 mM NaCl feed solution at 50% water recovery for CDI research. Using this separation, we compare the desalination performance of a flow-through electrode (fte-CDI) cell and a flow between membrane (fb-MCDI) device, showing how significantly different systems can be compared in terms of generally desirable desalination characteristics. In general, we find that performance analysis must be considered carefully so to not allow for ambiguous separation conditions or the maximization of one metric at the expense of another. Additionally, for context we discuss a number of important underlying performance indicators and cell characteristics that are not performance measures in and of themselves but can be examined to better understand differences in performance.

physics.chem-ph↗

arXiv2018

Frequency analysis and resonant operation for efficient capacitive deionization

Capacitive deionization (CDI) performance metrics can vary widely with operating methods. We here develop a theory around and experimentally demonstrate a new operation for CDI that uses sinusoidal forcing voltage (or sinusoidal current). We use a dynamic system modeling approach, and quantify the frequency response (amplitude and phase) of CDI effluent concentration, and demonstrate that CDI can be modeled as a linear time invariant system. We validate this model with experiments, and show that a sinusoid voltage operation can simultaneously achieve high salt removal and strong energy performance, thus very likely making it superior to other conventional operating methods. Based on the underlying coupled phenomena of electrical charge (and ionic) transfer with bulk advection in CDI, we derive and validate experimentally the concept of using sinusoidal voltage forcing functions to achieve resonance-type operation for CDI. Despite the complexities of the system, we find a simple relation for the resonant time scale: the resonant time period is proportional to the geometric mean of the flow residence time and the electrical (RC) charging time. Operation at resonance implies the optimal balance between absolute amount of salt removed (in moles) and dilution (depending on the feed volume processed), thus resulting in the maximum average concentration reduction for the desalinated water. Using a generalized tool based on Fourier analysis, we show that most of the salt removal (~95%) for square and triangular voltage forcing waveforms is achieved by the fundamental Fourier (sinusoidal) mode. The frequency of higher Fourier modes precludes high flow efficiency for these modes, so these modes consume additional energy for minimal additional salt removed. This deficiency of higher frequency modes further highlights the advantage of DC-offset sinusoidal forcing for CDI operation.

physics.chem-ph↗

arXiv2018

Thermodynamics of Ion Separation by Electrosorption

We present a simple, top-down approach for the calculation of minimum energy consumption of electrosorptive ion separation using variational form of the (Gibbs) free energy. We focus and expand on the case of electrostatic capacitive deionization (CDI), and the theoretical framework is independent of details of the double-layer charge distribution and is applicable to any thermodynamically consistent model, such as the Gouy-Chapman-Stern (GCS) and modified Donnan (mD) models. We demonstrate that, under certain assumptions, the minimum required electric work energy is indeed equivalent to the free energy of separation. Using the theory, we define the thermodynamic efficiency of CDI. We explore the thermodynamic efficiency of current experimental CDI systems and show that these are currently very low, less than 1% for most existing systems. We applied this knowledge and constructed and operated a CDI cell to show that judicious selection of the materials, geometry, and process parameters can be used to achieve a 9% thermodynamic efficiency (4.6 kT energy per removed ion). This relatively high value is, to our knowledge, by far the highest thermodynamic efficiency ever demonstrated for CDI. We hypothesize that efficiency can be further improved by further reduction of CDI cell series resistances and optimization of operational parameters.

physics.chem-ph↗

arXiv2017

Tailored Porous Electrode Resistance for Controlling Electrolyte Depletion and Improving Charging Response in Electrochemical Systems

The rapid charging and/or discharging of electrochemical cells can lead to localized depletion of electrolyte concentration. This depletion can significantly impact the system's time dependent resistance. For systems with porous electrodes, electrolyte depletion can limit the rate of charging and increase energy dissipation. Here we propose a theory to control and avoid electrolyte depletion by tailoring the value and spatial distribution of resistance in a porous electrode. We explore the somewhat counterintuitive idea that increasing local spatial resistances of the solid electrode itself leads to improved charging rate and minimal change in energy loss. We analytically derive a simple expression for an electrode resistance profile that leads to highly uniform electrolyte depletion. We use numerical simulations to explore this theory and simulate spatiotemporal dynamics of electrolyte concentration in the case of a supercapacitor with various tailored electrode resistance profiles which avoid localized depletion. This increases charging rate up to around 2-fold with minimal effect on overall dissipated energy in the system.

physics.chem-ph↗

arXiv2017

Isotachophoresis applied to chemical reactions

This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids, proteins, and live cells. ITP is a versatile technique which requires no specific geometric design or material, and is compatible with a wide range of microfluidic and automated platforms. Though ITP has traditionally been used as a purification and separation technique, recent years have seen its emergence as a method to automate and speed up chemical reactions. ITP has been used to demonstrate up to 14,000-fold acceleration of nucleic acid assays, and has been used to enhance lateral flow and other immunoassays, and even whole bacterial cell detection assays. We here classify these studies into two categories: homogeneous (all reactants in solution) and heterogeneous (at least one reactant immobilized on a solid surface) assay configurations. For each category, we review and describe physical modeling and scaling of ITP-aided reaction assays, and elucidate key principles in ITP assay design. We summarize experimental advances, and identify common threads and approaches which researchers have used to optimize assay performance. Lastly, we propose unaddressed challenges and opportunities that could further improve these applications of ITP.

q-bio.BM↗

arXiv2017

Nitrate removal from water using electrostatic regeneration of functionalized adsorbent

Nitrate is an important pollutant in drinking water worldwide, and a number of methods exist for the removal of nitrate from water including ion exchange and reverse osmosis. However, these approaches suffer from a variety of disadvantages including requirements for supply and disposal of brine used for regeneration in ion exchange and low water recovery ratio for reverse osmosis. Here, we demonstrate the use of high surface area activated carbon electrodes functionalized with moieties having high affinity for adsorption of nitrate from aqueous solution, such as those used in ion exchange. Adsorption of surfactant molecules having a quaternary amine ionic group to the activated carbon surfaces provides functionalization of the surfaces without complex chemistries. The functionalized electrodes have adsorption capacities of about 80 mg NaNO$_3$ per gram of activated carbon material. Unlike a traditional ion exchanger, the functionalized surfaces can be repeatedly regenerated by the application of an electrostatic potential which displaces the bound NO$_3^-$ while leaving an excess of electronic charge on the electrode. The cell is completed by an inert counter electrode where Faradaic reactions occur during regeneration. Up to approximately 40% of the initial capacity of the electrode is accessible following electrical regeneration.

physics.chem-ph↗

arXiv2015

Sensitivity analysis and study of the mixing uniformity of a microfluidic mixer

We consider a microfluidic mixer based on hydrodynamic focusing, which is used to initiate the folding process of individual proteins. The folding process is initiated by quickly diluting a local denaturant concentration, and we define mixing time as the time advecting proteins experience a specified to achieve a local drop in denaturant concentration. In previous work, we presented a minimization of mixing time which considered optimal geometry and flow conditions, and achieved a design with a predicted mixing time of 0.10 $μ$s. The aim of the current paper is twofold. First, we explore the sensitivity of mixing time to key geometric and flow parameters. In particular, we study the angle between inlets, the shape of the channel intersections, channel widths, mixer depth, mixer symmetry, inlet velocities, working fluid physical properties, and denaturant concentration thresholds. Second, we analyze the uniformity of mixing times as a function of inlet flow streamlines. We find the shape of the intersection, channel width, inlet velocity ratio, and asymmetries have strong effects on mixing time; while inlet angles, mixer depth, fluid properties, and concentration thresholds have weaker effects. Also, the uniformity of the mixing time is preserved for most of the inlet flow and distances of down to within about 0.4 $μ$m of the mixer wall. We offer these analyses of sensitivities to imperfections in mixer geometry and flow conditions as a guide to experimental efforts which aim to fabricate and use these types of mixers. Our study also highlights key issues and provides a guide to the optimization and practical design of other microfluidic devices dependent on both geometry and flow conditions.

physics.flu-dyn↗