15,052 research outputs found

    de Groot, Jan Willem B

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    The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study.

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    SummaryWe report on an atomistic molecular dynamics simulation of the complete conformational transition of Escherichia coli adenylate kinase (ADK) using the recently developed TEE-REX algorithm. Two phases characterize the transition pathway of ADK, which folds into the domains CORE and LID and the AMP binding domain AMPbd. Starting from the closed conformation, half-opening of the AMPbd precedes a partially correlated opening of the LID and AMPbd, defining the second phase. A highly stable salt bridge D118-K136 at the LID-CORE interface, contributing substantially to the total nonbonded LID-CORE interactions, was identified as a major factor that stabilizes the open conformation. Alternative transition pathways, such as AMPbd opening following LID opening, seem unlikely, as full transition events were not observed along this pathway. The simulation data indicate a high enthalpic penalty, possibly obstructing transitions along this route

    Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange

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    AbstractToday's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T0. This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references

    A Vertical Transport Geometry for Electrical Spin Injection and Extraction in Si

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    Schottky barriers formed between ferromagnetic metal and Semiconductor are of particular interest for spin injection and detection experiments. Here, we investigate electrical spin polarized carrier injection and extraction in Si using a Co/Si/Ni vertical structure built on a 250 nm thick Si membrane. Current-voltage measurements performed on the devices at low temperatures showed evidence of the conduction being dominated by thermionic field emission, which is believed to be the key to spin injection using Schottky junctions. This, however, proved inconclusive as our devices did not show any magnetoresistance signal even at low temperatures. We attribute this partially to the high resistance-area product in our Schottky contacts at spin injection biases. We show the potential of this vertical Spin-device for future experiments by numerical simulation. The results reveal that by growing a thin highly doped Ge layer at the Schottky junctions the resistancearea products could be tuned to obtain high magnetoresistance

    Historia y Cuadros de Costumbres

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    José Manuel Groot nació en Bogotá el 25 de diciembre de 1800 en el Virreinato de la Nueva Granada. Se desempeñó como pintor caricaturista, escritor costumbrista e historiador –considerado uno de los precursores de esta disciplina en el país. Murió el 3 de mayo de 1878. En este texto Groot, por un lado, retrata la cotidianidad de los santafereños: los pensamientos comunes, las costumbres y la vida social. Por otro lado, hace una innovación literaria para el momento, buscando reemplazar el estilo recargado de descripciones y sentimentalidades del Romanticismo, por descripciones más sobrias; con temáticas más cercanas a las realidades de los habitantes de la nación

    Dataset supporting the journal article 'Comprehensive analysis of radiative cooling enabled thermoelectric energy harvesting'

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    Data supporting the article &quot;Comprehensive analysis of radiative cooling enabled thermoelectric energy harvesting&quot; Yuxiao Zhu, Daniel W. Newbrook, C. H. de Groot and Ruomeng Huang. Journal of Physics: Photonics, Volume 5, Number 2, 025002, DOI 10.1088/2515-7647/accac1 The Data is an excel file containing raw data for the paper: Fig. 1 Schematic and temperature-dependent material properties of the N-type and P-type thermoelectric materials used in our RC-TEG model. ( Fig. 2 Temperature profile of the RC-TEG under typical working conditions. (a) exposed radiative surface (b) shielded counter surface. Fig. 3 FEM simulation performance of RC-TEG under various top surface convection (ConvT) and bottom surface convection (ConvB) conditions. Fig. 4 Performance of RC-TEG obtained in COMSOL simulation as a function of atmosphere emissivity (a) Temperature difference (&Delta;T) and (b) Power density (PDmax). Fig. 5 Performance of RC-TEG as a function of emissivity in the solar and thermal IR spectrum. Fig. 6 (a) Temperature difference, (b) Power (Pmax), (c) Power density (PDmax) obtained from COMSOL simulation as a function of pitch and WCooler. ( Fig. 7 (a) Temperature difference, (b) PDmax obtained from COMSOL simulation as a function of HTE and WTE. Fig. 8 (a) Real-time temperature and (b) solar irradiance of London on 1st July 2021, 11th January 2021, Singapore on 1st July 2021, and 1st January 2021. </span

    High quality Schottky contacts for limiting leakage currents in Ge-based Schottky barrier MOSFETs

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    Schottky barrier (SB) Ge channel MOSFETs suffer from high drain-body leakage at the required elevated substrate doping concentrations to suppress source-drain leakage. Here we show that electrodeposited Ni-Ge and NiGe/Ge Schottky diodes on highly doped Ge show low off current, which might make them suitable for SB p-MOSFETs. The Schottky diodes showed rectification of up to 5 orders in magnitude. At low forward biases the overlap of the forward current density curves for the as deposited Ni/n-Ge and NiGe/n-Ge Schottky diodes indicates Fermi-level pinning in the Ge band gap. The SB height for electrons remains virtually constant at 0.52 eV (indicating a hole barrier height of 0.14 eV) under various annealing temperatures. The series resistance decreases with increasing annealing temperature in agreement with four point probe measurements indicating the lower specific resistance of NiGe as compared to Ni, which is crucial for high drive current in SB p-MOSFETs. We show by numerical simulation that by incorporating such high quality Schottky diodes in the source/drain of a Ge channel PMOS, highly doped substrate could be used to minimize the subthreshold source to drain leakage current

    Asymmetric gate induced drain leakage and body leakage in vertical MOSFETs with reduced parasitic capacitance

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    Vertical MOSFETs, unlike conventional planar MOSFETs, do not have identical structures at the source and drain, but have very different gate overlaps and geometric configurations. This paper investigates the effect of the asymmetric source and drain geometries of surround-gate vertical MOSFETs on the drain leakage currents in the OFF-state region of operation. Measurements of gate-induced drain leakage (GIDL) and body leakage are carried out as a function of temperature for transistors connected in the drain-on-top and drain-on-bottom configurations. Asymmetric leakage currents are seen when the source and drain terminals are interchanged, with the GIDL being higher in the drain-on-bottom configuration and the body leakage being higher in the drain-on-top configuration. Band-to-band tunneling is identified as the dominant leakage mechanism for both the GIDL and body leakage from electrical measurements at temperatures ranging from ?50 to 200?C. The asymmetric body leakage is explained by a difference in body doping concentration at the top and bottom drain–body junctions due to the use of a p-well ion implantation. The asymmetric GIDL is explained by the difference in gate oxide thickness on the vertical (110) pillar sidewalls and the horizontal (100) wafer surface
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