Engineering of Bioenergy Crops: Dominant Genetic Approaches to Improve Polysaccharide Properties and Composition in Biomass.

Large-scale, sustainable production of lignocellulosic bioenergy from biomass will depend on a variety of dedicated bioenergy crops. Despite their great genetic diversity, prospective bioenergy crops share many similarities in the polysaccharide composition of their cell walls, and the changes needed to optimize them for conversion are largely universal. Therefore, biomass modification strategies that do not depend on genetic background or require mutant varieties are extremely valuable. Due to their preferential fermentation and conversion by microorganisms downstream, the ideal bioenergy crop should contain a high proportion of C6-sugars in polysaccharides like cellulose, callose, galactan, and mixed-linkage glucans. In addition, the biomass should be reduced in inhibitors of fermentation like pentoses and acetate. Finally, the overall complexity of the plant cell wall should be modified to reduce its recalcitrance to enzymatic deconstruction in ways that do no compromise plant health or come at a yield penalty. This review will focus on progress in the use of a variety of genetically dominant strategies to reach these ideals. Due to the breadth and volume of research in the field of lignin bioengineering, this review will instead focus on approaches to improve polysaccharide component plant biomass. Carbohydrate content can be dramatically increased by transgenic overexpression of enzymes involved in cell wall polysaccharide biosynthesis. Additionally, the recalcitrance of the cell wall can be reduced via the overexpression of native or non-native carbohydrate active enzymes like glycosyl hydrolases or carbohydrate esterases. Some research in this area has focused on engineering plants that accumulate cell wall-degrading enzymes that are sequestered to organelles or only active at very high temperatures. The rationale being that, in order to avoid potential negative effects of cell wall modification during plant growth, the enzymes could be activated post-harvest, and post-maturation of the cell wall. A potentially significant limitation of this approach is that at harvest, the cell wall is heavily lignified, making the substrates for these enzymes inaccessible and their activity ineffective. Therefore, this review will only include research employing enzymes that are at least partially active under the ambient conditions of plant growth and cell wall development

XH-stretching overtone transitions calculated using explicitly correlated coupled cluster methods

We have calculated XH-stretching (where X=O, C, F, Cl) fundamental and overtone transitions for three diatomics and a few small molecules using a local mode model. The potential energy curves and dipole moment functions are calculated using the recently developed explicitly correlated coupled cluster with single doubles and perturbative triples theory [CCSD_T_-F12] with the associated VXZ-F12 (where X=D, T, Q) basis sets. We find that the basis set convergence of calculated frequencies and oscillator strengths obtained with the explicitly correlated method is much more rapid than with conventional CCSD(T) and the Dunning type correlation consistent basis sets. Furthermore, CCSD(T)-F12 frequencies and oscillator strengths obtained with the VTZ-F12 and VQZ-F12 basis sets are found to be in excellent agreement with the CCSD(T) complete basis set limit. We find that comparison of CCSD(T)-F12 frequencies with experiment is less good. The inclusion of explicit correlation exposes the inherent error of the CCSD(T) method to overestimate vibrational frequencies, which is normally compensated by basis set incompleteness error. As a consequence, we suggest that conventional CCSD(T) in combination with the aug-cc-pVTZ or aug-cc-pVQZ basis sets is likely to yield calculated XH-stretching frequencies in closest agreement with experiment

Explicitly correlated intermolecular distances and interaction energies of hydrogen bonded complexes

We have optimized the lowest energy structures and calculated interaction energies for the H2O–H2O, H2O–H2S, H2O–NH3, and H2O–PH3 dimers with the recently developed explicitly correlated CCSD(T)-F12 methods and the associated VXZ-F12 (where X=D,T,Q) basis sets. For a given cardinal number, we find that the results obtained with the CCSD(T)-F12 methods are much closer to the CCSD(T) complete basis set limit than the conventional CCSD(T) results. In general we find that CCSD(T)-F12 results obtained with the VTZ-F12 basis set are better than the conventional CCSD(T) results obtained with an aug-cc-pV5Z basis set. We also investigate two ways to reduce the effects of basis set superposition error with conventional CCSD(T), namely, the popular counterpoise correction and limiting diffuse basis functions to the heavy atoms only. We find that for a given cardinal number, these selectively augmented correlation consistent basis sets yield results that are closer to the complete basis set limit than the corresponding fully augmented basis sets. Furthermore, we find that the difference between standard and counterpoise corrected interaction energies and intermolecular distances is reduced with the selectively augmented basis sets

Multiple Loop Self-Triggered Model Predictive Control for Network Scheduling and Control

We present an algorithm for controlling and scheduling multiple linear time-invariant processes on a shared bandwidth limited communication network using adaptive sampling intervals. The controller is centralized and computes at every sampling instant not only the new control command for a process, but also decides the time interval to wait until taking the next sample. The approach relies on model predictive control ideas, where the cost function penalizes the state and control effort as well as the time interval until the next sample is taken. The latter is introduced in order to generate an adaptive sampling scheme for the overall system such that the sampling time increases as the norm of the system state goes to zero. The paper presents a method for synthesizing such a predictive controller and gives explicit sufficient conditions for when it is stabilizing. Further explicit conditions are given which guarantee conflict free transmissions on the network. It is shown that the optimization problem may be solved off-line and that the controller can be implemented as a lookup table of state feedback gains. Simulation studies which compare the proposed algorithm to periodic sampling illustrate potential performance gains.Comment: Accepted for publication in IEEE Transactions on Control Systems Technolog

Identification of the dimethylamine-trimethylamine complex in the gas phase

We have identified the dimethylamine-trimethylamine complex (DMA-TMA) at room temperature in the gas phase. The Fourier transform infrared (FTIR) spectrum of DMA-TMA in the NH-stretching fundamental region was obtained by spectral subtraction of spectra of each monomer. Explicitly correlated coupled cluster calculations were used to determine the minimum energy structure and interaction energy of DMA-TMA. Frequencies and intensities of NH-stretching transitions were also calculated at this level of theory with an anharmonic oscillator local mode model. The fundamental NH-stretching intensity in DMA-TMA is calculated to be approximately 700 times larger than that of the DMA monomer. The measured and calculated intensity is used to determine a room temperature equilibrium constant of DMA-TMA of 1.7 × 10⁻³ atm⁻¹ at 298 K

On the Accuracy of Equivalent Antenna Representations

The accuracy of two equivalent antenna representations, near-field sources and far-field sources, are evaluated for an antenna installed on a simplified platform in a series of case studies using different configurations of equivalent antenna representations. The accuracy is evaluated in terms of installed far-fields and surface currents on the platform. The results show large variations between configurations. The root-mean-square installed far-field error is 4.4% for the most accurate equivalent representation. When using far-field sources, the design parameters have a large influence of the achieved accuracy. There is also a varying accuracy depending on the type of numerical method used. Based on the results, some recommendations on the choice of sub-domain for the equivalent antenna representation are given. In industrial antenna applications, the accuracy in determining e.g. installed far-fields and antenna isolation on large platforms are critical. Equivalent representations can reduce the fine-detail complexity of antennas and thus give an efficient numerical descriptions to be used in large-scale simulations. The results in this paper can be used as a guideline by antenna designers or system engineers when using equivalent sources

The Higgs mass derived from the U(3) Lie group

The Higgs mass value is derived from a Hamiltonian on the Lie group U(3) where we relate strong and electroweak energy scales. The baryon states of nucleon and delta resonances originate in specific Bloch wave degrees of freedom coupled to a Higgs mechanism which also gives rise to the usual gauge boson masses. The derived Higgs mass is around 125 GeV. From the same Hamiltonian we derive the relative neutron to proton mass ratio and the N and Delta mass spectra. All compare rather well with the experimental values. We predict scarce neutral flavor baryon singlets that should be visible in scattering cross sections for negative pions on protons, in photoproduction on neutrons, in neutron diffraction dissociation experiments and in invariant mass spectra of protons and negative pions in B-decays. The fundamental predictions are based on just one length scale and the fine structure constant. More particular predictions rely also on the weak mixing angle and the up-down quark flavor mixing matrix element. With differential forms on the measure-scaled wavefunction, we could generate approximate parton distribution functions for the u and d valence quarks of the proton that compare well with established experimental analysis.Comment: 18 pages, 13 figures, 3 table

Resolving the notorious case of conical intersections for coupled cluster dynamics

The motion of electrons and nuclei in photochemical events often involve conical intersections, degeneracies between electronic states. They serve as funnels for nuclear relaxation - on the femtosecond scale - in processes where the electrons and nuclei couple nonadiabatically. Accurate ab initio quantum chemical models are essential for interpreting experimental measurements of such phenomena. In this paper we resolve a long-standing problem in coupled cluster theory, presenting the first formulation of the theory that correctly describes conical intersections between excited electronic states of the same symmetry. This new development demonstrates that the highly accurate coupled cluster theory can be applied to describe dynamics on excited electronic states involving conical intersections.Comment: 8 pages and 3 figures and including supporting information (with corrections and improved notation