Search Results - (Author, Cooperation:N. J. Tao)

2016-03-05

Nature Publishing Group (NPG)

0028-0836

1476-4687

Biology

Chemistry and Pharmacology

Medicine

Natural Sciences in General

Physics

1089-7550

AIP Digital Archive

Physics

We have studied the Au(111) surface under potential control under water, 0.1 M HClO4 and 10 mM NaH2PO4 using scanning tunneling microscopy. The 22×(large-closed-square) reconstruction was observed, demonstrating that the reconstruction is stable in contact with aqueous solutions. The measured periodicity and z corrugation of the reconstruction are in good agreement with studies done in ultrahigh vacuum. The stability of the reconstruction was found to depend on surface potential (vs a silver quasi-reference electrode). We have also observed structures other than the 22×(large-closed-square) pattern.

Electronic Resource

1089-7623

AIP Digital Archive

Physics

Electrical Engineering, Measurement and Control Technology

A method for detecting surface plasmon resonance with high resolution (∼10−5 degrees or ∼10−8 refractive index units) and fast response time (1 μs) is described. In the method, light is focused through a prism onto a metal film on which molecules to be detected are adsorbed. The total internal reflection of the incident light is collected with a bicell photodetector instead of a single cell or an array of photodetectors that are widely used in previous works. The ratio of the differential signal to the sum signal of the bicell photodetector provides an accurate measurement of shift in surface plasmon resonance angle caused by the adsorption of molecules onto the metal films or by conformational changes in the adsorbed molecules. Using the method, we have studied subtle conformational changes in redox protein, cytochrome c, due to an electron transfer reaction. © 1999 American Institute of Physics.

Electronic Resource

1077-3118

AIP Digital Archive

Physics

A nonmechanical method for fabricating a metallic narrow constriction between two electrodes using electrochemical deposition is described. The width of the constriction can be adjusted by slowly dissolving metal atoms away or redepositing atoms onto the constriction which can be controlled flexibly by the electrodes' potentials. Well-defined plateaus near the integer numbers of the conductance quantum have been observed in these constrictions at room temperature. Since no mechanical movements are involved, this method has the potential of fabricating nanoconstrictions with long term stability. © 1998 American Institute of Physics.

Electronic Resource

1077-3118

AIP Digital Archive

Physics

We have studied molecular adsorption onto stable metallic nanowires fabricated with an electrochemical method. Upon the adsorption, the quantized conductance decreases, typically, to a fractional value, which may be attributed to the scattering of the conduction electrons by the adsorbates. The further conductance change occurs when the nanowire is exposed to another molecule that has stronger adsorption strength. Because the quantized conductance is determined by a few atoms at the narrowest portion of each nanowire, adsorption of a molecule onto the portion is enough to change the conductance, which may be used for chemical sensors. © 2000 American Institute of Physics.

Electronic Resource

1077-3118

AIP Digital Archive

Physics

We have studied electron tunneling across the gap between two electrodes as the gap is varied by electrodeposition and etching. The tunneling current tends to change in a stepwise fashion, corresponding to a discrete change of the gap width. The stepwise change is due to the discrete nature of atoms and a series of structural relaxations of the atoms at the electrodes between stable configurations upon deposition and etching. By stabilizing the tunneling current on various steps using a feedback loop, we have demonstrated that stable molecular-scale gaps can be fabricated with subangstrom precision. © 2000 American Institute of Physics.

Electronic Resource

1077-3118

AIP Digital Archive

Physics

We describe a method to fabricate atomic-scale gaps and contacts between two metal electrodes. The method uses a directional electrodeposition process and has a built-in self-termination mechanism. The final gap width and contact size are preset by an external resistor (Rext) that is connected in series to one of the electrodes. If 1/Rext is chosen to be much smaller than the conductance quantum (G0=2e2/h), a small gap with conductance determined by electron tunneling is formed. If 1/Rext is comparable or greater than G0, a contact with conductance near a multiple of G0 is fabricated. © 2002 American Institute of Physics.

Electronic Resource

1077-3118

AIP Digital Archive

Physics

We electrochemically deposit conducting polymer to bridge two closely placed electrodes, and then form a polymer nanowire by stretching the polymer bridge with the electrodes. During stretching, the conductance increases initially as the polymer chains are aligned in parallel, and then decreases in a stepwise fashion, due to abrupt changes in the nanowire thickness. We study the current–voltage (I–V) characteristics of the nanowire as a function of its electrochemical potential in an analogous fashion to the control of the gate voltage in semiconductor devices. Depending on the potential, the I–V curves vary from ohmic to rectifying characteristics. © 2001 American Institute of Physics.

Electronic Resource

1089-7690

AIP Digital Archive

Physics

Chemistry and Pharmacology

A combined experimental and theoretical study is conducted on guanine molecules adsorbed on graphite substrate. The main effort is to understand the scanning tunneling microscopic images and the effect of scanning tip force on guanine molecules and their images. The force on guanine molecule is determined from the tip-induced deformation in the substrate and is found to be a few nano-Newtons per guanine molecule. A jellium substrate is used to model the graphite substrate in ab initio calculations of electronic density of states. Both the equilibrium height of guanine and tip force on guanine are determined using pseudopotential density functional calculations of system's total energy. The calculated height of guanine molecule above the substrate is in good agreement with measurements. Electronic states are calculated and it is shown that features in surface density of states are mostly due to admixture with the guanine LUMO and the admixture increases with increasing scanning tip force. © 1996 American Institute of Physics.

Electronic Resource

1089-7623

AIP Digital Archive

Physics

Electrical Engineering, Measurement and Control Technology

We present an automated setup to measure the surface plasmon resonance (SPR)-enhanced optical absorption spectra of molecular adsorbates. The setup detects the reflectivity at the SPR resonance angle as a function of the incident light wavelength. Because the resonance angle is wavelength dependent, a feedback mechanism adjusts the photodetector position to follow the resonance angle when the wavelength varies. Both theoretical calculations and experimental measurements show a signal enhancement of up to ∼40 times over the conventional absorption spectroscopy. The SPR-based absorption spectroscopy is surface specific because the optical field is localized near the surface at resonance. In addition, the SPR angular shift is simultaneously measured, which provides adsorbate coverage and adsorption kinetic information. We anticipate that with our automated system, the method could be used in the study of adsorbed molecules and in chemical and biosensor applications. © 2001 American Institute of Physics.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

We have used Raman scattering to study the water O-H stretching modes at ∼ 3450 and ∼ 3220 cm-1 in DNA films as a function of relative humidity (r.h.). The intensity of the 3220-cm-1 band vanishes as the r.h. is decreased from 98% to around 80%, which indicates that the hydrogen-bond network of water is disrupted in the primary hydration shell (which therefore cannot have an “ice-like” structure). The number of water molecules in the primary hydration shell was determined from the intensity of the ∼ 3200-cm-1 band as about 30 water molecules per nucleotide pair. The ∼ 3400-cm-1 O-H stretch band was used for determining the total water content, and this band persists at 0% r.h., implying that 5-6 tightly bound water molecules per nucleotide pair remain. The frequency of the ∼ 3400-cm-1 O-H stretch mode is lower by 30 to 45 cm-1 in the primary hydration shell compared to free water. The water content as a function of r.h. obtained from these experiments agrees with gravimetric measurements. The disappearance of the ∼ 3200-cm-1 band and the shift of the ∼ 3400-cm-1 O-H stretch band provide a reliable way of measuring the hydration number of DNA.

7 Ill.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

3 Ill.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

We have used Brillouin scattering to measure the linewidths and frequencies of GHz acoustic phonons in Na- and Li-DNA films as a function of temperature between 300 and 140 K for samples that were dry, lightly, and heavily hydrated. The linewidths decrease with falling temperature and water contents, indicating that coupling to a water relaxation is the main source of phonon damping. The strength of the relaxation was determined using measurements of the phonon linewidth as a function of frequency, and confirmed by comparison of measured and calculated spectral profiles. The relaxation strength is anisotropic, being greater for phonons propagating perpendicular to the helix axis. The hydrated DNA exhibits both a rapid relaxation (≤ 10-11 s per radian) giving rise to a classical f2 damping, and a slower motion with a relaxation time that varies from ∼ 4 × 10-11 s per radian (primary hydration shell) to ∼ 2 × 10-12 s per radian (secondary hydration shell) at room temperature. In the frequency interval that bounds these relaxation times (∼ 4 to 80 GHz) we expect degrees of freedom associated with the primary hydration shell to be important. The sample with primary hydration follows a simple Arrhenius behavior with ΔH ∼ 5 kcal mole-1. The effective activation energy for the sample with secondary hydration is somewhat higher (indicating a more cooperative water relaxation) and varies strongly with temperature. The elastic moduli change much more than can be accounted for by relaxation, indicating the importance of water motion in softening interatomic potentials. The extent of the softening caused by the “unfreezing” of water motion is similar to the degree of softening caused by hydrating the sample.

6 Ill.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

We have used Brillouin spectroscopy to study the velocities and attenuation of acoustic phonons in wet-spun films of Na-DNA and Li-DNA as a function of the degree of hydration at room temperature. Our data for the longitudinal acoustic (LA) phonon velocity vs water content display several interesting features and reveal effects that we can model at the atomic level as interhelical bond softening and relaxation of the hydration shell. The model for interhelical softening makes use of other physical parameters of these films, which we have determined by gravimetric, x-ray, and optical microscopy studies. We extract intrinsic elastic constants for hydrated Na-DNA molecules of c11 ≃ 8.0 × 1010 dynes/cm2 and c33 ≃ 5.7 × 1010 dynes/cm2, which corresponds to a Young's modulus, E ≃ 1.1 × 1010 dynes/cm2 (with Poisson's ratio, σ = 0.44). The negative velocity anisotropy of the LA phonons indicates that neighboring DNA molecules are held together by strong interhelical bonds in the solid state. The LA phonon attenuation data can be understood by the relaxational model in which the acoustic phonon is coupled to a relaxation mode of the water molecules. Na-DNA undergoes the A to B phase transition at a relative humidity (rh) of 92% while Li-DNA (which remains in the B form in this range) decrystallizes at an rh of 84%. We find that our Brillouin results for Na- and Li-DNA are remarkably similar, indicating that the A to B phase transition does not play an important role in determining the acoustic properties of these two types of DNA.

7 Ill.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

We have studied the hydration of Na-DNA and Li-DNA fibers and films, measuring water contents, x-ray fiber diffraction patterns, low-frequency Raman spectra (below 100 cm-1), high-frequency Raman spectra (600-1000 cm-1), and swelling, as a function of relative humidity. Most samples gain weight equilibrium (though not conformational equilibrium) in one day. The volume occupied by a base pair as the DNA is hydrated (obtained from the x-ray and swelling data) shows anomalies for the case of Na-DNA in the region where the A-form occurs. Our Raman and x-ray data reproduce the well-known features of the established conformational transitions, but we find evidence in the Raman spectra and optical properties of a transition to what may be a disordered B-like conformation in Na-DNA below 40% relative humidity. We have studied the effects of crystallinity on the A to B transition. We find that the transition to the B-form is impeded in highly crystalline samples. In most samples, the transition occurs in three days (after putting the sample at 92% relative humidity) but in highly crystalline samples, the transition may take months. By comparing the high-frequency Raman spectra of highly ordered and disordered films, we show that the extent of crystallinity controls the amount of A-DNA formed when ethanol is used to dehydrate the films. We show that rapid dehydration (by laser heating) does not result in a B to A transition. A fiber that gives A-type x-ray reflections probably contains B-like material in noncrystalline regions. The low-frequency Raman spectrum is dominated by a band at about 25 cm-1 in both Na- and Li-DNA. Another band is seen near 35 cm-1 in Na-DNA at humidities where the sample is in the A-form. In contrast to earlier reports, we find that the Raman intensity does not depend on fiber orientation relative to the scattering vector. The “35-cm-1” band is largely depolarized (i.e. vertical polarization incident and horizontal polarization scattered, VH, or vice versa, HV) while the “25-cm-1” band appears in both VV, VH and HV polarizations. These bands are all weaker in HH polarization. The “25-cm-1” band may be due to a shearing motion of the phosphates and their associated counterions, while the “35-cm-1” band may be characteristic of A-DNA crystallites. We consider mass-loading, relaxational coupling to the hydration shell, and softening of interatomic potentials as possible explanations of the observed softening of the low-frequency Raman bands on hydration. Relaxation data suggest that the added water binds tightly (on these time scales) and a mass-loading model accounts for the observed softening rather well.We conclude that the A to B transition is not driven by softening of the “25-cm-1” band. Rather, it is most probably a consequence of crystal-packing forces, with the more regular A-form favored in crystals when these forces are strong.

10 Ill.

Electronic Resource

0006-3525

Chemistry ; Polymer and Materials Science

Wiley InterScience Backfile Collection 1832-2000

Chemistry and Pharmacology

We have measured the dispersion of phonon line widths between frequencies of about 2 and 10 GHz in DNA films at relative humidities between 0 and 95%. The results show that the relaxation mode of the primary hydration shell retains its basic characteristics even in samples with very high water content. A modified mode coupling model is used to include both the collective nature of the sound wave and to describe the change in hydration explicitly. It enables us to describe the coupling between the phonons and the water relaxation mode at various water contents, and allows us to extract values for the primary shell relaxation time and coupling constants over the range of hydration studied. The primary shell relaxation time (∼ 40 ps) and coupling parameters remain nearly constant over the entire range of hydration. We have reanalyzed our earlier Brillouin data (taken as a function of temperature) in terms of two relaxation processes (primary plus a secondary shell contribution of about 2 ps at room temperature). This new analysis indicates that both processes follow a simple Arrhenius behavior with activation energies of 5 kcal mole-1 for the primary relaxation and 7 kcal mole-1 for the secondary relaxation. We also observe a rather broad central mode that can be fitted by a Lorentzian, and that may arise from direct (as opposed to coupled-mode) scattering from the primary relaxation mode.

8 Ill.

Electronic Resource