Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools.

This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations

Theoretical analysis of electronic processes occurring during ultrafast demagnetization of cobalt triggered by X-ray photons tuned to Co L3_3 resonance

Magnetization dynamics triggered with ultrashort laser pulses has been attracting significant attention, with strong focus on the dynamics excited by VIS/NIR pulses. Only recently, strong magnetic response in solid materials induced by intense X-ray pulses from free-electron lasers (FELs) has been observed. The exact mechanisms that trigger the X-ray induced demagnetization are not yet fully understood. They are subject of on-going experimental and theoretical investigations. Here, we present a theoretical analysis of electronic processes occurring during demagnetization of Co multilayer system irradiated by X-ray pulses tuned to L$_3$-absorption edge of cobalt. We show that, similarly as in the case of X-ray induced demagnetization at M-edge of Co, electronic processes play a predominant role in the demagnetization until the pulse fluence does not exceed the structural damage threshold. The impact of electronic processes can reasonably well explain the available experimental data, without a need to introduce the mechanism of stimulated elastic forward scattering.Comment: 10 pages, 4 figures (7 panels), 57 references; pdfRevTeX class; double column formatting; two appendices and 18 references added; author-created version submitted to and accepted in Physical Review B journal. arXiv admin note: text overlap with arXiv:2202.1384

A Fully Tunable Single-Walled Carbon Nanotube Diode

We demonstrate a fully tunable diode structure utilizing a fully suspended single-walled carbon nanotube (SWNT). The diode's turn-on voltage under forward bias can be continuously tuned up to 4.3 V by controlling gate voltages, which is ~6 times the nanotube bandgap energy. Furthermore, the same device design can be configured into a backward diode by tuning the band-to-band tunneling current with gate voltages. A nanotube backward diode is demonstrated for the first time with nonlinearity exceeding the ideal diode. These results suggest that a tunable nanotube diode can be a unique building block for developing next generation programmable nanoelectronic logic and integrated circuits.Comment: 14 pages, 4 figure

Multifunctional Devices and Logic Gates With Undoped Silicon Nanowires

We report on the electronic transport properties of multiple-gate devices fabricated from undoped silicon nanowires. Understanding and control of the relevant transport mechanisms was achieved by means of local electrostatic gating and temperature dependent measurements. The roles of the source/drain contacts and of the silicon channel could be independently evaluated and tuned. Wrap gates surrounding the silicide-silicon contact interfaces were proved to be effective in inducing a full suppression of the contact Schottky barriers, thereby enabling carrier injection down to liquid-helium temperature. By independently tuning the effective Schottky barrier heights, a variety of reconfigurable device functionalities could be obtained. In particular, the same nanowire device could be configured to work as a Schottky barrier transistor, a Schottky diode or a p-n diode with tunable polarities. This versatility was eventually exploited to realize a NAND logic gate with gain well above one.Comment: 6 pages, 5 figure

Tachyon Hair on Two-Dimensional Black Holes

Static black holes in two-dimensional string theory can carry tachyon hair. Configurations which are non-singular at the event horizon have non-vanishing asymptotic energy density. Such solutions can be smoothly extended through the event horizon and have non-vanishing energy flux emerging from the past singularity. Dynamical processes will not change the amount of tachyon hair on a black hole. In particular, there will be no tachyon hair on a black hole formed in gravitational collapse if the initial geometry is the linear dilaton vacuum. There also exist static solutions with finite total energy, which have singular event horizons. Simple dynamical arguments suggest that black holes formed in gravitational collapse will not have tachyon hair of this type.Comment: 11 pages, 1 figure (not included), uses phyzzx, SU-ITP-93-1

Delayed Senescence in Soybean: Terminology, Research Update, and Survey Results from Growers

The terms used to describe symptoms of delayed senescence in soybean often are used inconsistently or interchangeably and do not adequately distinguish the observed symptoms in the field. Various causes have been proposed to explain the development of delayed senescence symptoms. In this article, we review published reports on delayed senescence symptoms in soybean, summarize current research findings, provide examples of terms related to specific symptoms, and present an overview of the results of a multi-state survey directed to soybean growers to understand their concerns about delayed soybean senescence. Some of these terms, such as green bean syndrome and green stem syndrome, describe symptoms induced by biotic factors, while other terms describe symptoms associated with abiotic factors. Some delayed senescence terms involve the whole plant remaining green while other terms include just the stem and other plant parts such as pods. In the grower survey, 77% reported observing soybean plants or plant parts that remained green after most plants in the field were fully mature with ripe seed. Most respondents attributed these symptoms to changes in breeding and choice of cultivars. At the end of this article, we standardized the terms used to describe delayed senescence in soybean

Bridging photochemistry and photomechanics with NMR crystallography: the molecular basis for the macroscopic expansion of an anthracene ester nanorod

Crystals composed of photoreactive molecules represent a new class of photomechanical materials with the potential to generate large forces on fast timescales. An example is the photodimerization of 9-tert-butyl-anthracene ester (9TBAE) in molecular crystal nanorods that leads to an average elongation of 8%. Previous work showed that this expansion results from the formation of a metastable crystalline product. In this article, it is shown how a novel combination of ensemble oriented-crystal solid-state NMR, X-ray diffraction, and first principles computational modeling can be used to establish the absolute unit cell orientations relative to the shape change, revealing the atomic-resolution mechanism for the photomechanical response and enabling the construction of a model that predicts an elongation of 7.4%, in good agreement with the experimental value. According to this model, the nanorod expansion does not result from an overall change in the volume of the unit cell, but rather from an anisotropic rearrangement of the molecular contents. The ability to understand quantitatively how molecular-level photochemistry generates mechanical displacements allows us to predict that the expansion could be tuned from +9% to −9.5% by controlling the initial orientation of the unit cell with respect to the nanorod axis. This application of NMR-assisted crystallography provides a new tool capable of tying the atomic-level structural rearrangement of the reacting molecular species to the mechanical response of a nanostructured sample