Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly

Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.

In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.

As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.

Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.

Gamma-ray induced color centers in Yb : YAG crystals grown by Czochralski method

20 at.% Yb:YAG single crystals have been grown by the CZ method and gamma-ray irradiation induced color centers and valence change of Fe3+ and Yb3+ ions in Yb:YAG have been studied. One significant 255 nm absorption band was observed in as-grown crystals and was attributed to Fe3+ ions. Two additional absorption (AA) bands located at 255 nm and 345 nm, respectively, were produced after gamma irradiation. The changes in the AA spectra after gamma irradiation and air annealing are mainly related to the charge exchange of the Fe3+, Fe2+, oxygen vacancies and F-type color centers. Analysis shows that the broad AA band is associated with Fe2+ ions and F-type color centers. The transition Yb3+ Yb2+ takes place as an effect of recharging of one of the Yb3+ ions from a pair in the process of gamma irradiation. (C) 2006 Elsevier Ltd. All rights reserved.

An experimental study of the mobility of edge dislocations in pure copper single crystals

The velocity of selectively-introduced edge dislocations in 99.999 percent pure copper crystals has been measured as a function of stress at temperatures from 66°K to 373°K by means of a torsion technique. The range of resolved shear stress was 0 to 15 megadynes/ cm^2 for seven temperatures (66°K, 74°K, 83°K, 123°K, 173°K, 296°K, 296°K, 373°K.

Dislocation mobility is characterized by two distinct features; (a) relatively high velocity at low stress (maximum velocities of about 9000 em/sec were realized at low temperatures), and (b) increasing velocity with decreasing temperature at constant stress.

The relation between dislocation velocity and resolved shear stress is:

v = v_o(τ_r/τ_o)^n

where v is the dislocation velocity at resolved shear stress τ_r, v_o is a constant velocity chosen equal to 2000 cm/ sec, τ_o is the resolved shear stress required to maintain velocity v_o, and n is the mobility coefficient. The experimental results indicate that τ_o decreases from 16.3 x 10^6 to 3.3 x 10^6 dynes/cm^2 and n increases from about 0.9 to 1.1 as the temperature is lowered from 296°K to 66°K.

The experimental dislocation behavior is consistent with an interpretation on the basis of phonon drag. However, the complete temperature dependence of dislocation mobility could not be closely approximated by the predictions of one or a combination of mechanisms.

Nonlinear Effects in Granular Crystals with Broken Periodicity

When studying physical systems, it is common to make approximations: the contact interaction is linear, the crystal is periodic, the variations occurs slowly, the mass of a particle is constant with velocity, or the position of a particle is exactly known are just a few examples. These approximations help us simplify complex systems to make them more comprehensible while still demonstrating interesting physics. But what happens when these assumptions break down? This question becomes particularly interesting in the materials science community in designing new materials structures with exotic properties In this thesis, we study the mechanical response and dynamics in granular crystals, in which the approximation of linearity and infinite size break down. The system is inherently finite, and contact interaction can be tuned to access different nonlinear regimes. When the assumptions of linearity and perfect periodicity are no longer valid, a host of interesting physical phenomena presents itself. The advantage of using a granular crystal is in its experimental feasibility and its similarity to many other materials systems. This allows us to both leverage past experience in the condensed matter physics and materials science communities while also presenting results with implications beyond the narrower granular physics community. In addition, we bring tools from the nonlinear systems community to study the dynamics in finite lattices, where there are inherently more degrees of freedom. This approach leads to the major contributions of this thesis in broken periodic systems. We demonstrate the first defect mode whose spatial profile can be tuned from highly localized to completely delocalized by simply tuning an external parameter. Using the sensitive dynamics near bifurcation points, we present a completely new approach to modifying the incremental stiffness of a lattice to arbitrary values. We show how using nonlinear defect modes, the incremental stiffness can be tuned to anywhere in the force-displacement relation. Other contributions include demonstrating nonlinear breakdown of mechanical filters as a result of finite size, and the presents of frequency attenuation bands in essentially nonlinear materials. We finish by presenting two new energy harvesting systems based on our experience with instabilities in weakly nonlinear systems.

Theoretical investigation of nonvolatile holographic storage in doubly doped lithium niobate crystals

We have studied theoretically the inherent mechanisms of nonvolatile holographic storage in doubly doped LiNbO3 crystals. The photochromic effect of doubly doped LiNbO3 crystals is discussed, and the criterion for this effect is obtained through the photochromism-bleach factor a = S(21)gamma(1)/S(11)gamma(2) that we define. The two-center recording and fixing processes are analytically discussed with extended Kukhtarev equations, and analytical expressions for recorded and fixed steady-state space-charge fields as well as temporal behavior during the fixing process are obtained. The effects of microphysical quantities, the macrophotochromic effect on fixing efficiency, and recorded and fixed steady-state space-charge fields, are discussed analytically and numerically. (C) 2002 Optical Society of America.

Nonvolatile photorefractive holograms in LiNbO3 : Cu : Ce crystals

We report experimental and theoretical studies of nonvolatile photorefractive holographic recording in LiNbO3:Cu:Ce crystals with two illumination schemes: (1) UV light for sensitization and a red interfering pattern for recording and (2) blue light for sensitization and a red pattern for recording. The results show that the oxidized LiNbO3:Cu:Ce crystals can provide high, persistent refractive-index modulation with weak lightinduced scattering. The optimal working conditions and the prescription for doping and oxidation-reduction processing that yields the maximum refractive-index modulation are discussed. (C) 2000 Optical Society of America OCIS codes: 050.7330, 190.5330, 090.2900.

Electrochromic effect in domain-inversion process LiNbO3 : Ru : Fe crystals

A reversible electrochromic effect accompanying domain-inversion during the electrical poling process in LiNbO3: Ru: Fe crystals at room temperature has been observed. In electrode area, both electrochromism and domain-inversion occur alternately, and electrochromism is also reversible during back-switch poling, which is experimentally verified and whose mechanism is briefly explained using a microstructure ferroelectric model. In addition, because of the enhancing elcctrochromic effect, different from the undoped LiNbO3 crystals, the coercive riled (21.0 kV/mm or so) measured in LiNbO3: Ru: Fe is lower than its breakdown field, thus providing a possible new technique for realizing the domain-inversion by constant electric field rather than a pulsed one.

Absorption characteristic and nonvolatile holographic recording in LiNbO3 : Cr : Cu crystals

The absorption characteristic of lithium niobate crystals doped with chromium and copper (Cr and Cu) is investigated. We find that there are two apparent absorption bands for LiNbO3:Cr:Cu crystal doped with 0.14 wt.% Cr2O3 and 0.011 wt.% CuO; one is around 480 nm, and the other is around 660 nm. With a decrease in the doping composition of Cr and an increase in the doping composition of Cu, no apparent absorption band in the shorter wavelength range exists. The higher the doping level of Cr, the larger the absorbance around 660 nm. Although a 633 nm red light is located in the absorption band around 660 nm, the absorption at 633 nm does not help the photorefractive process; i.e., unlike other doubly doped crystals, for example, LiNbO3:Fe:Mn crystal, a nonvolatile holographic recording can be realized by a 633 nm red light as the recording light and a 390 nm UV light as the sensitizing light. For LiNbO3:Cr:Cu crystals, by changing the recording light from a 633 nm red light to a 514 nm green light, sensitizing with a 390 nm UV light and a 488 nm blue light, respectively, a nonvolatile holographic recording can be realized. Doping the appropriate Cr (for example, N-Cr = 2.795 X 10(25)m(-3) and N-Cr/N-Cu = 1) benefits the improvement of holographic recording properties. (c) 2005 Optical Society of America.

Reversible electrochromic effect accompanying domain-inversion in LiNbO3 : Ru : Fe crystals

A reversible electrochromic effect during the electrical poling process in LiNbO3:Ru:Fe crystals at room temperature is observed. In electrode area, both electrochromism and domain-inversion occur mutually and electrochromism is reversible during back-switch poling, which are experimentally verified, and a microstructure model to explain the mechanism is proposed. In addition, different from the undoped LiNbO3 crystals, the breakdown field (> 25.0 kV/mm) is higher than the coercive (21.0 kV/mm) measured in LiNbO3:Ru:Fe, which proves a possible new technique to realize domain-inversion by constant electric field rather than pulsed one. (c) 2005 American Institute of Physics.

Improvement of sensitivity and refractive-index changes in LiNbO3 : Ce : Cu crystals with UV light

A nonvolatile recording scheme is proposed using LiNbO3:Ce:Cu crystals and modulated UV light to record gratings simultaneously in two centres and using red light to bleach the grating in the shallow centre to realize persistent photorefractive holographic storage. Compared with the normal UV-sensitized nonvolatile holographic system, the amplitude of refractive-index changes is greatly increased and the recording sensitivity is significantly enhanced by recording with UV light in the LiNbO3:Ce:Cu crystals. Based on jointly solving the two-centre material equations and the coupled-wave equations, temporal evolutions of the photorefractive grating and the diffraction effciency are effectively described and numerically analysed. Roles of doping levels and recording-beam intensity are discussed in detail. Theoretical results confirm and predict experimental results.