Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge-Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E coli, and conclude with a discussion on the significance of this work. (C) 2004 Elsevier Ltd. All rights reserved.

Study of the initial stage of solid electrolyte interphase formation upon chemical reaction of lithium metal and N-Methyl-N-Propyl-Pyrrolidinium-Bis (Fluorosulfonyl) Imide

Chemical reaction studies of N-methyl-N-propyl-pyrrolidinium-bis(fluorosulfonyl)imide-based ionic liquid with the lithium metal surface were performed using ab initio molecular dynamics (aMD) simulations and X-ray Photoelectron Spectroscopy (XPS). The molecular dynamics simulations showed rapid and spontaneous decomposition of the ionic liquid anion, with subsequent formation of long-lived species such as lithium fluoride. The simulations also revealed the cation to retain its structure by generally moving away from the lithium surface. The XPS experiments showed evidence of decomposition of the anion, consistent with the aMD simulations and also of cation decomposition and it is envisaged that this is due to the longer time scale for the XPS experiment compared to the time scale of the aMD simulation. Overall experimental results confirm the majority of species suggested by the simulation. The rapid chemical decomposition of the ionic liquid was shown to form a solid electrolyte interphase composed of the breakdown products of the ionic liquid components in the absence of an applied voltage.

Double diffusive Marangoni convection flow of electrically conducting fluid in a square cavity with chemical reaction

Double diffusive Marangoni convection flow of viscous incompressible electrically conducting fluid in a square cavity is studied in this paper by taking into consideration of the effect of applied magnetic field in arbitrary direction and the chemical reaction. The governing equations are solved numerically by using alternate direct implicit (ADI) method together with the successive over relaxation (SOR) technique. The flow pattern with the effect of governing parameters, namely the buoyancy ratio W, diffusocapillary ratio w, and the Hartmann number Ha, is investigated. It is revealed from the numerical simulations that the average Nusselt number decreases; whereas the average Sherwood number increases as the orientation of magnetic field is shifted from horizontal to vertical. Moreover, the effect of buoyancy due to species concentration on the flow is stronger than the one due to thermal buoyancy. The increase in diffusocapillary parameter, w caus

Effect of surface resistance on gas absorption accompanied by a chemical reaction in a gas - liquid contactor

An analysis of gas absorption accompanied by chemical reaction in the presence of interfacial resistance is presented. The analysis indicates that the effect of interfacial resistance on interphase mass transfer is significantly higher in presence of a reaction compared to the pure absorption case. For fixed values of surface resistance and contact time, the difference between the amount of gas transferred across the interface with and without surface resistance increases as the value of reaction velocity increases. For ranges of contact time and surface resistance of practical relevance, the influence of surface resistance is too high to be neglected while designing gas-liquid contactors.

Mass transfer with chemical reaction in a foam bed contactor

On the basis of dodecahedral structure of a foam bed, a model to predict conversion in a foam bed contactor with mass transfer with chemical reaction has been developed. To verify the proposed model, experiments have been carried out in a semi-batch apparatus for the absorption of lean CO2 gas in a foam of sodium hydroxide solution. The proposed model predicts fairly well the experimentally found absorption values.

A model for doped-oxide-source diffusion with a chemical reaction at the silicon-silicon dioxide interface

A mathematical model for doped-oxide-source diffusion is proposed. In this model the concept of segregation of impurity at the silicon-silicon dioxide is used and also a constant of “rate limitation” is introduced through a chemical reaction at the interface.

On Application Of The Method Of Kinetic Invariants To The Description Of Dissolution Accompanied By A Chemical Reaction

The dissolution, accompanied by chemical reaction, of monodisperse solid particles has been analysed. The resulting model, which accounts for the variation of mass transfer coefficient with the size of the dissolving particles, yields an approximate analytical form of a kinetic function. Rigorous numerical and approximate analytical solutions have been obtained for the governing system of nonlinear ordinary differential equations. The transient nature of the dissolution process as well as the accuracy of the analytical solution is brought out by the rigorous numerical solution. The analytical solution is fairly accurate for the major part of the range of operational times encountered in practice.

Sonochemical reaction engineering

Ultrasound has been widely used by chemists to enhance yields as well as rates of homogeneous as well as heterogeneous chemical reactions. The effect of ultrasound on the course of chemical reactions is mediated through cavitation bubbles it generates. High temperatures and pressures are attained inside the cavitating bubbles when they collapse. The extreme conditions so generated lead to the formation of reactive intermediates, e.g., free radiacls, inside the bubbles, which cause chemical reactions to occur when they enter the surrounding liquid. This is the mechanism through which ultrasound influences the path of homogeneous reactions. The cavitation bubbles collapse asymmetrically in the vicinity of solids, e.g., catalyst particles. Asymmetric collapse lead to formation of high speed microjets. The microjets can enhance transport rates, the increase surface area through pitting as well as particle fragmentation through collisions. Both can alter the rates of heterogeneous reaction rates. It however appears that these effects do not exhaust the scope of the influence of ultrasound on heterogeneous reactions. Modelling and quantitative prediction of the effect of ultrasound on chemical reactions is however at a stage of infancy as the phenomena are complex. Only a few examples of modelling exist in literature. Apart from this, reactor design and scaleup pose significant problems. Thus sonochemical reaction engineering offers large scope for research and development efforts.

Some Basic Aspects of Reaction Engineering of Precipitation Processes

Analysis of precipitation reactions is extremely important in the technology of production of fine particles from the liquid phase. The control of composition and particle size in precipitation processes requires careful analysis of the several reactions that comprise the precipitation system. Since precipitation systems involve several, rapid ionic dissociation reactions among other slower ones, the faster reactions may be assumed to be nearly at equilibrium. However, the elimination of species, and the consequent reduction of the system of equations, is an aspect of analysis fraught with the possibility of subtle errors related to the violation of conservation principles. This paper shows how such errors may be avoided systematically by relying on the methods of linear algebra. Applications are demonstrated by analyzing the reactions leading to the precipitation of calcium carbonate in a stirred tank reactor as well as in a single emulsion drop. Sample calculations show that supersaturation dynamics can assume forms that can lead to subsequent dissolution of particles that have once been precipitated.

Comments on ``Influence of chemical reaction and viscous dissipation on MHD mixed convection flow'' by K. Das JMST 28 (5) (2014) 1881 similar to 1885] and ``Cu-water nanofluid flow and heat transfer over a shrinking sheet'' by K. Das JMST 28 (12) 5089 similar to 5094]

In this letter, we submit our comment on the following recently published papers by Kalidas Das: (1) ``Influence of chemical reaction and viscous dissipation on MHD mixed convection flow,'' Journal of Mechanical Science and Technology 28 (5) (2014) 1881-1885; and (2) ``Cu-water nanofluid flow and heat transfer over a shrinking sheet,'' Journal of Mechanical Science and Technology 28 (12) (2014) 5089-5094. The authors attempt to present the similarity solutions in both papers. We comment that the similarity transformations considered in Refs. 1, 2] are incorrect. Thus, the results presented by Kalidas Das lead to invalid conclusions.

Chronopotentiometry with power-law perturbation functions at an expanding plane electrode with and without a preceding blank period for systems with a coupled first-order homogeneous chemical reaction

The systems formalism is used to obtain the interfacial concentration transients for power-law current input at an expanding plane electrode. The explicit results for the concentration transients obtained here pertain to arbitrary homogeneous reaction schemes coupled to the oxidant and reductant of a single charge-transfer step and the power-law form without and with a preceding blank period (for two types of power-law current profile, say, (i) I(t) = I0(t−t0)q for t greater-or-equal, slanted t0, I(t) = 0 for t < t0; and (ii) I(t) = I0tq for t greater-or-equal, slanted t0, I(t) = 0 for t < t0). Finally the potential transients are obtained using Padé approximants. The results of Galvez et al. (for E, CE, EC, aC) (J. Electroanal. Chem., 132 (1982) 15; 146 (1983) 221, 233, 243), Molina et al. (for E) (J. Electroanal. Chem., 227 (1987) 1 and Kies (for E) (J. Electroanal. Chem., 45 (1973) 71) are obtained as special cases.

Numerical Simulation of Gaseous Detonation of H_2-O_2 Mixture with Detailed Chemical Reaction Model

采用高精度的ENO格式和基于基元化学反应的真实化学反应模型求解氢氧混合气体一维爆轰波的精细结构。采用直接起爆方法得到稳定传播的爆轰波,计算的爆轰波阵面参数和实验相当符合。对爆轰波反应区化学反应的研究表明,参与反应的不同组分具有不同类型的变化特征。网格尺寸影响的研究表明,计算结果的精度随着网格尺寸的增加而增加,并能保持较好的收敛性。移动网格研究结果表明,网格运动速度和爆轰速度接近时,两者的相互作用对计算结果产生一定影响。

Microscopic theory of chemical-reaction rate

In this paper we deduce the formulae for rate-constant of microreaction with high resolving power of energy from the time-dependent Schrdinger equation for the general case when there is a depression on the reaetional potential surface (when the depression is zero in depth, the case is reduced to that of Eyring). Based on the assumption that Bolzmann distribution is appropriate to the description of reactants, the formula for the constant of macrorate in a form similar to Eyring's is deduced and the expression for the coefficient of transmission is given. When there is no depression on the reactional potential surface and the coefficient of transmission does not seriously depend upon temperature, it is reduced to Eyring's. Thus Eyring's is a special case of the present work.