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Biomedical subjects

Richard N Zare

Publications and source records attributed to Richard N Zare.

At least 19 recordsLinked to original sources
PubMed2007

Counting low-copy number proteins in a single cell.

We have designed a microfluidic device in which we can manipulate, lyse, label, separate, and quantify the protein contents of a single cell using single-molecule fluorescence counting. Generic labeling of proteins is achieved through fluorescent-antibody binding. The use of cylindrical optics enables high-efficiency (approximately 60%) counting of molecules in micrometer-sized channels. We used this microfluidic device to quantify beta2 adrenergic receptors expressed in insect cells (SF9). We also analyzed phycobiliprotein contents in individual cyanobacterial cells (Synechococcus sp. PCC 7942) and observed marked differences in the levels of specific complexes in cell populations that were grown under nitrogen-depleted conditions.

Animals↗
PubMed2006

Organics captured from comet 81P/Wild 2 by the Stardust spacecraft.

Organics found in comet 81P/Wild 2 samples show a heterogeneous and unequilibrated distribution in abundance and composition. Some organics are similar, but not identical, to those in interplanetary dust particles and carbonaceous meteorites. A class of aromatic-poor organic material is also present. The organics are rich in oxygen and nitrogen compared with meteoritic organics. Aromatic compounds are present, but the samples tend to be relatively poorer in aromatics than are meteorites and interplanetary dust particles. The presence of deuterium and nitrogen-15 excesses suggest that some organics have an interstellar/protostellar heritage. Although the variable extent of modification of these materials by impact capture is not yet fully constrained, a diverse suite of organic compounds is present and identifiable within the returned samples.

Carbon↗
PubMed2006

Construction and calibration of an instrument for three-dimensional ion imaging.

We describe a new instrument based on a delay-line detector for imaging the complete three-dimensional velocity distribution of photoionized products from photoinitiated reactions. Doppler-free [2+1] resonantly enhanced multiphoton ionization (REMPI) of H and D atoms formed upon photolysis of HBr and DBr in the range 203 nm < or = lambda photolysis < or = 243 nm yields radial speeds measured to be accurate within 1% of those calculated. The relative speed resolution is about 5% and limited by photoionization recoil broadening. A relative speed resolution of 3.4% is obtained for [3+1] REMPI, which minimizes the ionization recoil. We also determine the branching ratio between ground-state and spin-orbit-excited product channels and their associated anisotropies. We find that DBr photolysis dynamics differs slightly from its HBr counterpart.

Journal Article↗
PubMed2006

Controlling electroosmotic flow in poly(dimethylsiloxane) separation channels by means of prepolymer additives.

The electroosmotic flow (EOF) in a poly(dimethylsiloxane) (PDMS) separation channel can be altered and controlled by adding a carboxylic acid to the prepolymer prior to curing. When the prepolymer is doped with 0.5 wt % undecylenic acid (UDA), the electroosmotic mobility in a modified PDMS channel rises to (7.6 +/- 0.2) x 10(-4) cm(2) V(-1) s(-1) (in HEPES buffer at pH 8.5), which is nearly twice that in the native PDMS channel. Because this modification does not significantly change the hydrophobicity of the PDMS surface, it is possible to combine the modified PDMS with a dynamic coating of n-dodecyl beta-d-maltoside (DDM), which prevents protein sticking (see Huang, B.; Wu, H. K.; Kim, S.; Zare, R. N. Lab Chip 2005, 5, 1005-1007). The modified PDMS channel with a dynamic coating of DDM generates an electroosmotic mobility of (5.01 +/- 0.09) x 10(-4) cm(2) V(-1) s(-1), which shows excellent reproducibility both in successive runs and during storage in water. Combining this surface modification and the dynamic coating of DDM is an effective means for both providing stable EOF in the PDMS channels and preventing protein adsorption on the channel walls. To demonstrate these effects, we show that the electrophoretic separation of immunocomplexes in free solution can be readily accomplished in a microfluidic chip made of UDA-doped (0.5 wt %) PDMS with a dynamic coating of DDM.

Dimethylpolysiloxanes↗
PubMed2006

On-line biological sample cleanup for electrospray mass spectrometry using sol-gel columns.

Using a slight overpressure, a urine sample is loaded onto a monolithic photopolymerized sol-gel column that has been derivatized with hydrophobic carbon chains and then the complex urine matrix is washed with aqueous solution. A buffer containing organic solvent is used to elute the adsorbed peptides by an applied voltage and the sample is then introduced into a mass spectrometer by sheath flow electrospray. The importance of desalting this type of sample is demonstrated by an experiment that shows that the signal intensity of a test solution with neurotensin, sprayed directly into the mass spectrometer, decreased from 4.5x10(4) cps to no detectible signal when just 10% urine is added to the sample solution. We suggest that this procedure may find general application for desalting biological samples prior to mass spectrometric analysis.

Chromatography, Liquid↗
PubMed2006

Generation of complex, static solution gradients in microfluidic channels.

A microfluidic device is used to generate a complex gradient of diffusible molecules in a static solution. The gradient is precise and steady both in space and in time. This device, made from poly(dimethylsiloxane), consists of three layers. The molecules in reservoirs on the top layer diffuse through the flat middle layer of hydrogel and reach an equilibrium distribution. Microfluidic channels on the bottom layer that are in close contact with the hydrogel contain free solution that has concentration gradients based on the gradient in the gel. The gradient profile in the channel can be designed to have an arbitrary form (within the range of the existing gradient in the hydrogel) by controlling the local direction of the channel at each point.

Dimethylpolysiloxanes↗
PubMed2006

H + CD4 abstraction reaction dynamics: product energy partitioning.

This paper presents experimental and theoretical studies of the product energy partitioning associated with the H + CD4 (nu = 0) --> HD + CD3 reaction for the collision energy range 0.5-3.0 eV. The theoretical results are based on quasiclassical trajectories from (1) first principles direct dynamics calculations (B3LYP/6-31G), (2) an empirical surface developed by Espinosa-García [J. Chem. Phys. 2002, 116, 10664] (EG), and (3) two semiempirical surfaces (MSINDO and reparametrized MSINDO). We find that most of the energy appears in product translation at energies just above the reactive threshold; however, HD vibration and rotation become quite important at energies above 1 eV, each accounting for over 20% of the available energy above 1.5 eV, according to the B3LYP calculations. The barrier on the B3LYP surface, though being later than that on EG, predicts significantly higher HD vibrational excitation than EG. This deviation is contradictory to what would be expected on the basis of the Polanyi rules and derives from modest differences in the potential energy surfaces. The CD3 internal energy is generally quite low, and we present detailed rotational state distributions which show that the CD3 rotational distribution is largely independent of collision energy in the 0.75-1.95 eV range. The most populated rotational levels are N = 5 and 6 on B3LYP, with most of that excitation being associated with motion about the C2 axes, rather than C3 axis, of the CD3 product, in good agreement with the experimental results. Through our extensive studies in this and previous work concerning the scattering dynamics, we conclude that B3LYP/6-31G provides the best available description of the overall dynamics for the title reaction at relatively high collision energies.

Journal Article↗
PubMed2006

Phospholipid biotinylation of polydimethylsiloxane (PDMS) for protein immobilization.

Polydimethylsiloxane (PDMS) surfaces can be functionalized with biotin groups by adding biotinylated phospholipids to the PDMS prepolymer before curing. The addition of beta-D-dodecyl-N-maltoside (DDM) in the solution blocks non-specific protein binding on these functionalized PDMS surfaces. We characterize the surface by measuring fluorescently labeled streptavidin binding. Single molecule tracking shows that the phospholipids are not covalently linked to PDMS polymer chains, but the surface functionalization is not removed by washing. We demonstrate the immobilization of biotinylated antibodies and lectins through biotin-avidin interactions.

Avidin↗
PubMed2006

Comparing reactions of H and Cl with C-H stretch-excited CHD3.

We report the methyl radical product state distributions for the reactions of H and Cl with CHD3(nu1 = 1,2) at collision energies of 1.53 and 0.18 eV, respectively. Both reactions demonstrate mode selectivity. The resulting state distributions from the H+CHD3(nu1 = 1,2) reactions are well described by a spectator model. The reactions Cl + CHD3(nu1 = 1,2) exhibit similar behavior, but in some aspects the spectator model breaks down. We attribute this breakdown to enhanced intramolecular vibrational redistribution in the Cl + CHD3(nu1 = 1,2) reactions compared to the H + CHD3(nu1 = 1,2) reactions, caused by the interaction of the slower Cl atom with the vibrationally excited CHD3, which is promoted either by its longer collision duration, its stronger coupling, or both.

Journal Article↗
PubMed2006

H + CD4 abstraction reaction dynamics: excitation function and angular distributions.

We compare experimental photoloc measurements and quasi-classical trajectory calculations of the integral cross sections, lab-frame speed distributions, and angular distributions associated with the CD3 products of the H + CD4(nu = 0) --> CD3 + HD reaction at collision energies ranging from 0.5 to 3.0 eV. Of the potential energy surfaces (PES) we explored, the direct dynamics calculations using the B3LYP/6-31G** density functional theory PES provide the best agreement with the experimental measurements. This agreement is likely due to the better overall description that B3LYP provides for geometries well removed from the minimum energy path, even though its barrier height is low by approximately 0.2 eV. In contrast to previous theoretical calculations, the angular distributions on this surface show behavior associated with a stripping mechanism, even at collision energies only approximately 0.1 eV above the reaction barrier. Other potential energy surfaces, which include an analytical potential energy surface from Espinosa-García and a direct dynamics calculation based on the MSINDO semiempirical Hamiltonian, are less accurate and predict more rebound dynamics at these energies than is observed. Reparametrization of the MSINDO surface, though yielding better agreement with the experiment, is not sufficient to capture the observed dynamics. The differences between these surfaces are interpreted using an analysis of the opacity functions, where we find that the wider cone of acceptance on the B3LYP surface plays a crucial role in determining the integral cross sections and angular distributions.

Journal Article↗
PubMed2005

Reaction products with internal energy beyond the kinematic limit result from trajectories far from the minimum energy path: an example from H + HBr --> H2 + Br.

The importance of reactive trajectories straying far from the minimum energy path is demonstrated for the bimolecular reaction H + HBr --> H2(v', j') + Br at 53 kcal/mol collision energy. Product quantum state distributions are measured and calculated using the quasi-classical trajectory technique, and the calculations indicate that highly internally excited H2 products result from indirect reactive trajectories with bent transition states. A general argument is made suggesting that reaction products with internal energy exceeding a kinematic constraint can, in general, be attributed to reactive collisions straying far from the minimum energy path.

Journal Article↗
PubMed2005

Cytochrome c conformations resolved by the photon counting histogram: watching the alkaline transition with single-molecule sensitivity.

We apply the photon counting histogram (PCH) model, a fluorescence technique with single-molecule sensitivity, to study pH-induced conformational changes of cytochrome c. PCH is able to distinguish different protein conformations based on the brightness of a fluorophore sensitive to its local environment. We label cytochrome c through its single free cysteine with tetramethylrhodamine-5-maleimide (TMR), a fluorophore with specific brightnesses that we associate with specific protein conformations. Ensemble measurements demonstrate two different fluorescence responses with increasing pH: (i) a decrease in fluorescence intensity caused by the alkaline transition of cytochrome c (pH 7.0-9.5), and (ii) an increase in intensity when the protein unfolds (pH 9.5-10.8). The magnitudes of these two responses depend strongly on the molar ratio of TMR used to label cytochrome c. Using PCH we determine that this effect arises from the proportion of a nonfunctional conformation in the sample, which can be differentiated from the functional conformation. We further determine the causes of each ensemble fluorescence response: (i) during the alkaline transition, the fluorophore enters a dark state and discrete conformations are observed, and (ii) as cytochrome c unfolds, the fluorophore incrementally brightens, but discrete conformations are no longer resolved. Moreover, we also show that functional TMR-cytochrome c undergoes a response of identical magnitude regardless of the proportion of nonfunctional protein in the sample. As expected for a technique with single-molecule sensitivity, we demonstrate that PCH can directly observe the most relevant conformation, unlike ensemble fluorometry.

Alkalies↗
PubMed2005

Undulatory delamination of thin polymer films on gold surfaces.

Using two-dimensional surface plasmon resonance measurements, we have observed the formation of traveling waves in the delamination of thin films of polydimethylsilane (PDMS) exposed to methanol. Films were spin-coated on a gold surface and the methanol was added to the top surface. The stress-induced instability caused by the swelling of the PDMS thin film when its edge is pinned to the gold surface leads to wrinkle formation and propagation at the interface. The periodic pattern is thought to be the result of an Asaro-Tiller-Grinfeld (ATG) instability.

Crystallization↗
PubMed2005

Construction of microfluidic chips using polydimethylsiloxane for adhesive bonding.

A thin layer of polydimethylsiloxane (PDMS) prepolymer, which is coated on a glass slide, is transferred onto the embossed area surfaces of a patterned substrate. This coated substrate is brought into contact with a flat plate, and the two structures are permanently bonded to form a sealed fluidic system by thermocuring (60 degrees C for 30 min) the prepolymer. The PDMS exists only at the contact area of the two surfaces with a negligible portion exposed to the microfluidic channel. This method is demonstrated by bonding microfluidic channels of two representative soft materials (PDMS substrate on a PDMS plate), and two representative hard materials (glass substrate on a glass plate). The effects of the adhesive layer on the electroosmotic flow (EOF) in glass channels are calculated and compared with the experimental results of a CE separation. For a channel with a size of approximately 10 to 500 microm, a approximately 200-500 nm thick adhesive layer creates a bond without voids or excess material and has little effect on the EOF rate. The major advantages of this bonding method are its generality and its ease of use.

Adhesiveness↗
PubMed2005

Effects of C-H stretch excitation on the H+CH4 reaction.

We have investigated the effects of C-H stretching excitation on the H+CH4-->CH3+H2 reaction dynamics using the photo-LOC technique. The CH3 product vibrational state and angular distribution are measured for the reaction of fast H atoms with methane excited in either the antisymmetric stretching fundamental (nu3=1) or first overtone (nu3=2) with a center-of-mass collision energy of Ecoll ranging from 1.52 to 2.20 eV. We find that vibrational excitation of the nu3=1 mode enhances the overall reaction cross section by a factor of 3.0+/-1.5 for Ecoll=1.52 eV, and this enhancement factor is approximately constant over the 1.52-2.20-eV collision energy range. A local-mode description of the CH4 stretching vibration, in which the C-H oscillators are uncoupled, is used to describe the observed state distributions. In this model, the interaction of the incident H atom with either a stretched or an unstretched C-H oscillator determines the vibrational state of the CH3 product. We also compare these results to the similar quantities obtained previously for the Cl+CH4-->CH3+HCl reaction at Ecoll=0.16 eV [Z. H. Kim, H. A. Bechtel, and R. N. Zare, J. Chem. Phys. 117, 3232 (2002); H. A. Bechtel, J. P. Camden, D. J. A. Brown, and R. N. Zare, ibid. 120, 5096 (2004)] in an attempt to elucidate the differences in reactivity for the same initially prepared vibration.

Journal Article↗
PubMed2005

Duty cycle and modulation efficiency of two-channel Hadamard transform time-of-flight mass spectrometry.

Hadamard transform time-of-flight mass spectrometry (HT-TOFMS) is based on the pseudorandom gating of ion packets into a time-of-flight mass-to-charge analyzer. In its typical implementation, the technique is able to monitor continuous ion sources with a 50% duty cycle, independent of all other figures of merit. Recently, we have demonstrated that the duty cycle can be extended to 100% using patterned, two-channel detection. Two-channel HT-TOFMS involves the simultaneous optimization of paired one-channel experiments and imposes more stringent conditions to achieve high-quality spectra. An ion modulation device, known as Bradbury-Nielson Gate (BNG), is central to HT-TOFMS. It is an ideal deflection plate, capable of transmitting or deflecting an ion beam according to a known binary sequence without changing the times-of-flight of the ions. Analytical equations are derived that accurately describe the ion modulation process of the BNG as confirmed by good agreement with SimIon simulations and ion beam imaging experiments. From these expressions, the duty cycle and ion modulation efficiency were calculated for various BNG parameters, ion beam characteristics, and detector dimensions, which permit the optimum conditions to be chosen for the two-channel experiment. We conclude that the outer detector should be three times the maximum deflection angle to detect all deflected ions (100% duty cycle) and that the difference between the modulated ion counts in the sequence elements 0 and 1 should be maximized to achieve high modulation efficiency. This condition is best achieved by tight focusing of the ion beam in the center of the inner detector. When both channels are optimized, the two-channel advantage can be exploited to achieve a further improvement over a single-channel experiment.

Algorithms↗