Current Size Limit Research Articles

Chemical Synthesis of Modified RNA.

Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.

Chemical Synthesis of Modified RNA

AbstractRibonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner—both in vitro and in vivo—are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site‐specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid‐phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4‐acetylcytidine, 5‐hydroxymethylcytidine, 3‐methylcytidine, 2′‐OCF3, and 2′‐N3 ribose modifications. We also discuss the all‐chemical synthesis of 5′‐capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single‐molecule FRET studies. Finally, we highlight promising developments in RNA‐catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.

Hyperbolic plasmons on natural biphenylene surface

Meta-surfaces constructed of patterned graphene nanoribbons on dielectric substrates have enabled in-plane propagation of surface plasmons with hyperbolic dispersion. However, the current size limitations of these meta-surface result in a restricted ceiling for the plasmon wave vector, highlighting the importance of exploring natural hyperbolic surfaces that do not require structuring. Here, we unveil a promising natural hyperbolic surface: the newly-synthesized graphene allotrope – biphenylene (BPN) [Fan et al., Science 372, 852–856 (2021)]. We demonstrate the anisotropic framework of π orbitals of BPN endows broadband hyperbolic plasmons on the BPN surface. Undamped plasmons emerge along the x-direction with a broadband spectrum from THz to the ultraviolet regime, whereas those along the y-direction are restricted to a low frequency region (<0.74 eV). Notably, hyperbolic regimes are observed within specific energy ranges, 1.21–2.44 eV and 3.35–3.51 eV, which facilitate the directional propagation of surface plasmons with hyperbolic dispersion relations. These results open an avenue for the use of graphene technique in advanced optics and offer a promising strategy for designing hyperbolic natural surfaces.

Quantum image processing on real superconducting and trapped-ion based quantum computers

Abstract The size and number of images and the amount of data we process every day have grown rapidly over the last years. Quantum computers promise to process this data more efficiently since classical images can be stored in quantum states. Experiments on quantum computer simulators prove the paradigms this promise is built on to be correct. However, currently, running the very same algorithms on a real quantum computer is often too error-prone to be of any practical use. We explore the current possibilities for image processing on real quantum computers. We redesign a commonly used quantum image encoding technique to reduce its susceptibility to errors. We show experimentally that the current size limit for images to be encoded on a quantum computer and subsequently retrieved with an error of at most 5 % is 2 × 2 pixels. A way to circumvent this limitation is to combine ideas of classical filtering with a quantum algorithm operating locally, only. We show the practicability of this strategy using the application example of edge detection. Our hybrid filtering scheme’s quantum part is an artificial neuron, working well on real quantum computers, too.

Toward Accurate Theoretical Vibrational Spectra: A Case Study for Maleimide.

We employ and combine a number of recent developments in vibrational structure methods to push their current size limitations toward molecules with tens of modes and showcase their availability for the maleimide molecule. In particular, we assess the use of different rectilinear vibrational coordinates, namely, normal coordinates, hybrid optimized and localized coordinates, and flexible adaptation of local coordinates of nuclei coordinates. These different coordinate parameterizations are employed in conjunction with the adaptive density-guided approach to generate potential energy surfaces (PESs). A screening procedure is furthermore introduced, which provides estimates of the importance of individual terms in the PES, resulting in significant reductions in the computational cost of the PES construction. We find that all three sets of coordinates provide approximately the same level of accuracy in vibrational structure calculations and report fundamental excitation energies with a mean absolute deviation of less than 12 cm-1 when compared to experimental data. We expect that similar accuracy in vibrational structure calculations can be achieved for molecules of larger size using the proposed procedures.

Gating Classical Information Flow via Equilibrium Quantum Phase Transitions.

The development of communication channels at the ultimate size limit of atomic scale physical dimensions will make the use of quantum entities an imperative. In this regime, quantum fluctuations naturally become prominent and are generally considered to be detrimental. Here, we show that for spin-based information processing, these fluctuations can be uniquely exploited to gate the flow of classical binary information across a magnetic chain in thermal equilibrium. Moreover, this information flow can be controlled with a modest external magnetic field that drives the system through different many-body quantum phases in which the orientation of the final spin does or does not reflect the orientation of the initial input. Our results are general for a wide class of anisotropic spin chains that act as magnetic cellular automata and suggest that quantum phase transitions play a unique role in driving classical information flow at the atomic scale.

Can optimal trap mesh size be predicted from body depth in a laterally-compressed fish species?

We used fish body depth to predict trap center-to-center mesh sizes that would optimize size selection of black sea bass Centropristis striata for both current and proposed minimum size limits for this species. We fished trap types of five different square mesh sizes/configurations: (1) 38.1mm mesh, (2) 38.1mm mesh on five sides and 50.8mm mesh on one side (back panel trap), (3) 50.8mm mesh, (4) 57.2mm mesh, and (5) 63.5mm mesh. The 38.1mm mesh trap was the control trap type. Back panel traps are the minimally legal mesh configuration in this region while 50.8mm mesh traps are commonly used in this fishery to further reduce culling of sub-legal black sea bass by fishers. Two previously untested mesh sizes, 57.2 and 63.5mm, were evaluated because a previously published morphometric relationship between black sea bass body depth and total length (TL) predicted that the diagonal openings of these two respective mesh sizes would retain black sea bass close to the current (279mm) and proposed minimum TL limits (305mm). We estimated size selection of each experimental trap type by comparing catches of control and experimental traps. All but the back panel trap displayed relatively steep selection around the fish length at which 50% of individuals were selected (l50). Initial size at retention (l10) by the 57.2 and 63.5mm trap types were nearly identical to current and proposed minimum fish sizes, respectively. Predictions from the body depth: TL relationship were very similar to estimates of l10 and l50, based on uncompressed body depth and compression to 93%. The 57.2mm mesh and 63.5mm mesh trap types maintained catches of legal fish but reduced catches of sub-legal fish compared to the back panel and 50.8mm mesh trap types. Relative to back panel and 50.8mm mesh traps, use of 57.2mm mesh traps would reduce rates of discard and discard mortality given current size limits in this fishery.

ATP consumption in molecular reactions of neuronal signaling

The human brain consumes 106 times less energy than the currently fastest supper computer [1], while maintaining a comparable performance in many demanding task [2]. These energetic efficiency has been suggested to result from primitive computations on a molecular level [3]. However, while the importance of ion channels on energy efficiency has been the primary focus of research [4,5], most computations occur at the molecular level prior to the amplification step and prior to the information transmission. We calculate the amount of energy consumed by such computations and compare their structural and functional properties. As a starting point, we chose the molecular reactions involved in long term depression and using our stochastic model [6] estimate the molecular energy consumption. To compare our feedback loop we investigate the energy consumption of millions of feedback loops in molecular signaling. For the first time we are able to go beyond the current size limit of 15 steps [7] and, using a computer cluster, detect feedback loops with hundreds of molecular reactions. We find that the number of ATPs consumed is related with size of positive feedback loop. We conclude that the energy consumed by the long term depression is only marginally above the physical limit of storing information and higher than its silicon equivalent of random access memory. Hence, this study provides the first systematic attempt to investigate the energy consumption of information-storing primitive computations and points towards energy efficient motifs for synthetic biology.

Temporal Changes in Size at Maturity and Their Implications for Fisheries Management for Eastern Bering Sea Tanner Crab

Tanner crab (Chionoecetes bairdi) in the eastern Bering Sea are primarily distributed in Bristol Bay and around the Pribilof Islands. Summer trawl survey data in these two areas were used to estimate mean sizes at maturity for female Tanner crab from 1975 to 2006 and sizes at 50% morphometric maturity for male Tanner crab from 1990 to 2006. Estimated mean sizes at maturity for females showed a statistically significant downward trend in both areas. Sizes at 50% morphometric maturity for males have declined significantly since 1990, in Bristol Bay only. In Bristol Bay, the distribution centers of female Tanner crab have shifted southwest over time and the decrease in female mean size at maturity was significantly related to changes in longitude and bottom depths. Because of terminal molt at maturity, the decrease in size at maturity has important implications for fisheries management: under the current size limit, a smaller proportion of males grow to legal size and therefore a higher proportion of large-growing males are removed by the fishery before they have a chance to participate in reproduction. With the recent maturity at a small size, reduction of the current harvest rates and size limit while maintaining current fishing gear requirements will result in higher yield and higher male spawning biomass per recruit than those under the current harvest strategy.

Dual beam generation at a ray caustic by a multiplexing computer-generated hologram

Computer generated holograms (CGHs) are used for testing aspherical surfaces. They are also used for certifying null lens systems that are in turn used to test large aspheric mirrors. We demonstrate that, in order to minimize size, a null-corrector-certifying CGH can be located at a ray caustic. This placement minimizes the required size of the CGH and so makes it possible to certify some null correctors that otherwise, due to current size limitations of high-precision CGHs, could not be certified. Fabrication limits of precision CGHs are in the size range of 200-250 mm and one part in 10;5 in feature placement. Our proof of principle involves a CGH that is about 20mm in diameter with a fabrication tolerance of one part in 10;4.

Encapsulation of an 86-kDa Assembly Intermediate inside the Cavities of GroEL and Its Single-ring Variant SR1 by GroES

We described previously that during the assembly of the alpha(2)beta(2) heterotetramer of human mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD), chaperonins GroEL/GroES interact with the kinetically trapped heterodimeric (alphabeta) intermediate to facilitate conversion of the latter to the native BCKD heterotetramer. Here, we show that the 86-kDa heterodimeric intermediate possesses a native-like conformation as judged by its binding to a fluorescent probe 1-anilino-8-naphthalenesulfonate. This large heterodimeric intermediate is accommodated as an entity inside cavities of GroEL and its single-ring variant SR1 and is encapsulated by GroES as indicated by the resistance of the heterodimer to tryptic digestion. The SR1-alphabeta-GroES complex is isolated as a stable single species by gel filtration in the presence of Mg-ATP. In contrast, an unfolded BCKD fusion protein of similar size, which also resides in the GroEL or SR1 cavity, is too large to be capped by GroES. The cis-capping mechanism is consistent with the high level of BCKD activity recovered with the GroEL-alphabeta complex, GroES, and Mg-ATP. The 86-kDa native-like heterodimeric intermediate in the BCKD assembly pathway represents the largest protein substrate known to fit inside the GroEL cis cavity underneath GroES, which significantly exceeds the current size limit of 57 kDa established for unfolded proteins.

MBE growth and device processing of MWIR HgCdTe on large area Si substrates

The traditional substrate of choice for HgCdTe material growth has been lattice matched bulk CdZnTe material. However, as larger array sizes are required for future devices, it is evident that current size limitations of bulk substrates will become an issue and therefore large area Si substrates will become a requirement for HgCdTe growth in order to maintain the cost-efficiency of future systems. As a result, traditional substrate mounting methods that use chemical compounds to adhere the substrate to the substrate holder may pose significant technical challenges to the growth and fabrication of HgCdTe on large area Si substrates. For these reasons, non-contact (indium-free) substrate mounting was used to grow mid-wave infrared (MWIR) HgCdTe material on 3″ CdTe/Si substrates. In order to maintain a constant tepilayer temperature during HgCdTe nucleation, reflection high-energy electron diffraction (RHEED) was implemented to develop a substrate temperature ramping profile for HgCdTe nucleation. The layers were characterized ex-situ using Fourier transform infrared (FTIR) and etch pit density measurements to determine structural characteristics. Dislocation densities typically measured in the 9 106 cm−2 to 1 107 cm−2 range and showed a strong correlation between ramping profile and Cd composition, indicating the uniqueness of the ramping profiles. Hall and photoconductive decay measurements were used to characterize the electrical properties of the layers. Additionally, both single element and 32 32 photovoltaic devices were fabricated from these layers. A RA value of 1.8 106-cm2 measured at −40 mV was obtained for MWIR material, which is comparable to HgCdTe grown on bulk CdZnTe substrates.

Small-cluster study of interacting fermions on a square lattice with next-nearest-neighbour interactions

We calculate the ground state energies and wavefunctions for small systems of interacting fermions on a square lattice with cylindrical topology. We examine the role of next-nearest-neighbour interactions on the observed ground states: the fractional quantum Hall ground state and the super-conducting ground state. Several different probes of fermion-pairing and off-diagonal long-range order as flux quantization, binding energies, pair-correlation functions and critical external magnetic field are investigated. Antiperiodic boundary conditions imposed in one direction provide a test of our numerical results within current size limitations.