Coarse Approach Research Articles

Drought Influence over Radial Growth of Mexican Conifers Inhabiting Mesic and Xeric Sites

Drought is a major constraint of forest productivity and tree growth across diverse habitat types. In this study, we investigated the drought responses of four conifer species growing within two locations of differing elevation and climatic conditions in northern Mexico. Two species were selected at a mesic site (Cupressus lusitanica Mill., Abies durangensis Martínez) and the other two species were sampled at a xeric site (Pinus engelmannii Carr., Pinus cembroides Zucc.). Using a dendrochronological approach, we correlated the radial-growth series of each species and the climatic variables. All study species positively responded to wet-cool conditions during winter and spring. Despite the close proximity of species at a mesic site, A. durangensis had high responsiveness to hydroclimatic variability, but C. lusitanica was not responsive. At the xeric site, P. engelmannii and P. cembroides were very responsive to drought severity, differentiated only by the longer time scale of the response to accumulated drought of P. engelmannii. The responsiveness to hydroclimate and drought of these tree species seems to be modulated by site conditions, or by the functional features of each species that are still little explored. These findings indicate that differentiating between mesic and xeric habitats is a too coarse approach in diverse forests with a high topographic heterogeneity.

Compact Scanning Tunneling Microscope with Large Scale Searching Capability for Mmultidisciplinary Applications

We present the design and performance of a home-built scanning tunneling microscope (STM), which is compact (66 mm tall and 25 mm in diameter), yet equipped with a 3D atomic precision piezoelectric motor in which the Z coarse approach relies on a high simplicity friction-type walker (of our own invention) driven by an axially cut piezoelectric tube. The walker is vertically inserted in a piezoelectric scanner tube (PST) with its brim laying flat on the PST end as the inertial slider (driven by the PST) for the XY (sample plane) motion. The STM is designed to be capable of searching rare microscopic targets (defects, dopants, boundaries, nano-devices, etc.) in a macroscopic sample area (square millimeters) under extreme conditions (low temperatures, strong magnetic fields, etc.) in which it fits. It gives good atomic resolution images after scanning a highly oriented pyrolytic graphite sample in air at room temperature.

Atomic resolution scanning tunneling microscope imaging up to 27 T in a water-cooled magnet

We report the first atomically resolved scanning tunneling microscope (STM) imaging in a water-cooled magnet (WM), for which extremely harsh vibrations and noise have been the major challenge. This custom WM-STM features an ultra-rigid and compact scan head in which the coarse approach is driven by our newly designed TunaDrive piezoelectric motor. A three-level spring hanging system is used for vibration isolation. Room-temperature raw-data images of graphite with quality atomic resolution were acquired in the presence of very strong magnetic fields, with a field strength up to 27 T, in a 32-mm-diameter bore WM with a maximum field strength of 27.5 T at a power rating of 10 MW, calibrated by nuclear magnetic resonance (NMR). This record field strength of 27 T exceeds the maximal field strength achieved by the conventional superconducting magnets. Besides, our WM-STM has paved the way to STM imaging using a 45 T, 32-mm-diameter bore hybrid magnet, which is the world’s flagship magnet, producing the strongest steady magnetic field.

A high stability and repeatability electrochemical scanning tunneling microscope.

We present a home built electrochemical scanning tunneling microscope (ECSTM) with very high stability and repeatability. Its coarse approach is driven by a closely stacked piezo motor of GeckoDrive type with four rigid clamping points, which enhances the rigidity, compactness, and stability greatly. It can give high clarity atomic resolution images without sound and vibration isolations. Its drifting rates in XY and Z directions in solution are as low as 84 pm/min and 59 pm/min, respectively. In addition, repeatable coarse approaches in solution within 2 mm travel distance show a lateral deviation less than 50 nm. The gas environment can be well controlled to lower the evaporation rate of the cell, thus reducing the contamination and elongating the measurement time. Atomically resolved SO4(2-) image on Au (111) work electrode is demonstrated to show the performance of the ECSTM.

A compact high field magnetic force microscope.

We present the design and performance of a simple and compact magnetic force microscope (MFM), whose tip-sample coarse approach is implemented by the piezoelectric tube scanner (PTS) itself. In brief, a square rod shaft is axially spring-clamped on the inner wall of a metal tube which is glued inside the free end of the PTS. The shaft can thus be driven by the PTS to realize image scan and inertial stepping coarse approach. To enhance the inertial force, each of the four outer electrodes of the PTS is driven by an independent port of the controller. The MFM scan head is so compact that it can easily fit into the 52mm low temperature bore of a 20T superconducting magnet. The performance of the MFM is demonstrated by imaging a manganite thin film at low temperature and in magnetic fields up to 15T.

Interaction Study of an Amorphous Solid Dispersion of Cyclosporin A in Poly-Alpha-Cyclodextrin with Model Membranes by (1)H-, (2)H-, (31)P-NMR and Electron Spin Resonance.

The properties of an amorphous solid dispersion of cyclosporine A (ASD) prepared with the copolymer alpha cyclodextrin (POLYA) and cyclosporine A (CYSP) were investigated by 1H-NMR in solution and its membrane interactions were studied by 1H-NMR in small unilamellar vesicles and by 31P 2H NMR in phospholipidic dispersions of DMPC (dimyristoylphosphatidylcholine) in comparison with those of POLYA and CYSP alone. 1H-NMR chemical shift variations showed that CYSP really interacts with POLYA, with possible adduct formation, dispersion in the solid matrix of the POLYA, and also complex formation. A coarse approach to the latter mechanism was tested using the continuous variations method, indicating an apparent 1 : 1 stoichiometry. Calculations gave an apparent association constant of log Ka = 4.5. A study of the interactions with phospholipidic dispersions of DMPC showed that only limited interactions occurred at the polar head group level (31P). Conversely, by comparison with the expected chain rigidification induced by CYSP, POLYA induced an increase in the fluidity of the layer while ASD formation led to these effects almost being overcome at 298 K. At higher temperature, while the effect of CYSP seems to vanish, a resulting global increase in chain fluidity was found in the presence of ASD.

Improving the accuracy of walking piezo motors.

Many application areas require ultraprecise, stiff, and compact actuator systems with a high positioning resolution in combination with a large range as well as a high holding and pushing force. One promising solution to meet these conflicting requirements is a walking piezo motor that works with two pairs of piezo elements such that the movement is taken over by one pair, once the other pair reaches its maximum travel distance. A resolution in the pm-range can be achieved, if operating the motor within the travel range of one piezo pair. However, applying the typical walking drive signals, we measure jumps in the displacement up to 2.4 μm, when the movement is given over from one piezo pair to the other. We analyze the reason for these large jumps and propose improved drive signals. The implementation of our new drive signals reduces the jumps to less than 42 nm and makes the motor ideally suitable to operate as a coarse approach motor in an ultra-high vacuum scanning tunneling microscope. The rigidity of the motor is reflected in its high pushing force of 6.4 N.

Facility for low-temperature spin-polarized-scanning tunneling microscopy studies of magnetic/spintronic materials prepared in situ by nitride molecular beam epitaxy.

Based on the interest in, as well as exciting outlook for, nitride semiconductor based structures with regard to electronic, optoelectronic, and spintronic applications, it is compelling to investigate these systems using the powerful technique of spin-polarized scanning tunneling microscopy (STM), a technique capable of achieving magnetic resolution down to the atomic scale. However, the delicate surfaces of these materials are easily corrupted by in-air transfers, making it unfeasible to study them in stand-alone ultra-high vacuum STM facilities. Therefore, we have carried out the development of a hybrid system including a nitrogen plasma assisted molecular beam epitaxy/pulsed laser epitaxy facility for sample growth combined with a low-temperature, spin-polarized scanning tunneling microscope system. The custom-designed molecular beam epitaxy growth system supports up to eight sources, including up to seven effusion cells plus a radio frequency nitrogen plasma source, for epitaxially growing a variety of materials, such as nitride semiconductors, magnetic materials, and their hetero-structures, and also incorporating in situ reflection high energy electron diffraction. The growth system also enables integration of pulsed laser epitaxy. The STM unit has a modular design, consisting of an upper body and a lower body. The upper body contains the coarse approach mechanism and the scanner unit, while the lower body accepts molecular beam epitaxy grown samples using compression springs and sample skis. The design of the system employs two stages of vibration isolation as well as a layer of acoustic noise isolation in order to reduce noise during STM measurements. This isolation allows the system to effectively acquire STM data in a typical lab space, which during its construction had no special and highly costly elements included, (such as isolated slabs) which would lower the environmental noise. The design further enables tip exchange and tip coating without breaking vacuum, and convenient visual access to the sample and tip inside a superconducting magnet cryostat. A sample/tip handling system is optimized for both the molecular beam epitaxy growth system and the scanning tunneling microscope system. The sample/tip handing system enables in situ STM studies on epitaxially grown samples, and tip exchange in the superconducting magnet cryostat. The hybrid molecular beam epitaxy and low temperature scanning tunneling microscopy system is capable of growing semiconductor-based hetero-structures with controlled accuracy down to a single atomic-layer and imaging them down to atomic resolution.

Design and control of a piezoelectric driven reticle assist device for prevention of reticle slip in lithography systems

This paper presents a device for managing the inertial loads on photoreticles of lithography scanners. At high scan accelerations, the reticle inertial load can approach the clamp force limit. As a result, nanometer-level presliding slip can occur. Reticle slip is one limitation on increasing the throughput of the lithography scanners. In this paper, we present a reticle assist device which can eliminate reticle slip by compensating better than 95% of the inertial loads when tested in a bench-top tester. The reticle assist device consists of a coarse approach mechanism, for accommodating reticle load/unload, and a piezoelectric stack for fine actuation. The device utilizes a sensorless control system design. The control system uses a self-sensing contact detection method, which is inspired by self-sensing scanning probe microscopy, to find the reticle edge. It also uses a charge amplifier with a novel hybrid hysteresis compensation technique to linearly control the piezoelectric actuator extension, without the need for closed-loop position control. When tested with a replicated force profile with 60N peak force and 6400N/s force rate, the assist device compensated better than 95% of the inertial load.

Design and properties of a cryogenic dip-stick scanning tunneling microscope with capacitive coarse approach control

We present the design, setup, and operation of a new dip-stick scanning tunneling microscope. Its special design allows measurements in the temperature range from 4.7K up to room temperature, where cryogenic vacuum conditions are maintained during the measurement. The system fits into every (4)He vessel with a bore of 50mm, e.g., a transport dewar or a magnet bath cryostat. The microscope is equipped with a cleaving mechanism for cleaving single crystals in the whole temperature range and under cryogenic vacuum conditions. For the tip approach, a capacitive automated coarse approach is implemented. We present test measurements on the charge density wave system 2H-NbSe2 and the superconductor LiFeAs which demonstrate scanning tunneling microscopy and spectroscopy data acquisition with high stability, high spatial resolution at variable temperatures and in high magnetic fields.

A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability

We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices.

Online appendix 1:Vegetation change (1988–2010) in Camdeboo National Park (South Africa), using fixed-point photo monitoring: The role of herbivory and climate

Fixed-point photo monitoring supplemented by animal census data and climate monitoring potential has never been explored as a long-term monitoring tool for studying vegetation change in the arid and semi-arid national parks of South Africa. The long-term (1988–2010), fixed-point monitoring dataset developed for the Camdeboo National Park, therefore, provides an important opportunity to do this. Using a quantitative estimate of the change in vegetation and growth form cover in 1152 fixed-point photographs, as well as series of step-point vegetation surveys at each photo monitoring site, this study documented the extent of vegetation change in the park in response to key climate drivers, such as rainfall, as well as land use drivers such as herbivory by indigenous ungulates. We demonstrated the varied response of vegetation cover within three main growth forms (grasses, dwarf shrubs [< 1 m] and tall shrubs [> 1 m]) in three different vegetation units and landforms (slopes, plains, rivers) within the Camdeboo National Park since 1988. Sites within Albany Thicket and Dwarf Shrublands showed the least change in vegetation cover, whilst Azonal vegetation and Grassy Dwarf Shrublands were more dynamic. Abiotic factors such as drought and flooding, total annual rainfall and rainfall seasonality appeared to have the greatest influence on growth form cover as assessed from the fixed-point photographs. Herbivory appeared not to have had a noticeable impact on the vegetation of the Camdeboo National Park as far as could be determined from the rather coarse approach used in this analysis and herbivore densities remained relatively low over the study duration.Conservation implications: We provided an historical assessment of the pattern of vegetation and climatic trends that can help evaluate many of South African National Parks’ biodiversity monitoring programmes, especially relating to habitat change. It will help arid parks in assessing the trajectories of vegetation in response to herbivory, climate and management interventions.

A coarse grain model for protein-surface interactions

The interaction of proteins with surfaces is important in numerous applications in many fields-such as biotechnology, proteomics, sensors, and medicine--but fundamental understanding of how protein stability and structure are affected by surfaces remains incomplete. Over the last several years, molecular simulation using coarse grain models has yielded significant insights, but the formalisms used to represent the surface interactions have been rudimentary. We present a new model for protein surface interactions that incorporates the chemical specificity of both the surface and the residues comprising the protein in the context of a one-bead-per-residue, coarse grain approach that maintains computational efficiency. The model is parameterized against experimental adsorption energies for multiple model peptides on different types of surfaces. The validity of the model is established by its ability to quantitatively and qualitatively predict the free energy of adsorption and structural changes for multiple biologically-relevant proteins on different surfaces. The validation, done with proteins not used in parameterization, shows that the model produces remarkable agreement between simulation and experiment.

Vegetation change (1988–2010) in Camdeboo National Park (South Africa), using fixed-point photo monitoring: The role of herbivory and climate

Fixed-point photo monitoring supplemented by animal census data and climate monitoring potential has never been explored as a long-term monitoring tool for studying vegetation change in the arid and semi-arid national parks of South Africa. The long-term (1988–2010), fixed-point monitoring dataset developed for the Camdeboo National Park, therefore, provides an important opportunity to do this. Using a quantitative estimate of the change in vegetation and growth form cover in 1152 fixed-point photographs, as well as series of step-point vegetation surveys at each photo monitoring site, this study documented the extent of vegetation change in the park in response to key climate drivers, such as rainfall, as well as land use drivers such as herbivory by indigenous ungulates. We demonstrated the varied response of vegetation cover within three main growth forms (grasses, dwarf shrubs [< 1 m] and tall shrubs [> 1 m]) in three different vegetation units and landforms (slopes, plains, rivers) within the Camdeboo National Park since 1988. Sites within Albany Thicket and Dwarf Shrublands showed the least change in vegetation cover, whilst Azonal vegetation and Grassy Dwarf Shrublands were more dynamic. Abiotic factors such as drought and flooding, total annual rainfall and rainfall seasonality appeared to have the greatest influence on growth form cover as assessed from the fixed-point photographs. Herbivory appeared not to have had a noticeable impact on the vegetation of the Camdeboo National Park as far as could be determined from the rather coarse approach used in this analysis and herbivore densities remained relatively low over the study duration.Conservation implications: We provided an historical assessment of the pattern of vegetation and climatic trends that can help evaluate many of South African National Parks’ biodiversity monitoring programmes, especially relating to habitat change. It will help arid parks in assessing the trajectories of vegetation in response to herbivory, climate and management interventions.

A scanning tunneling microscope capable of imaging specified micron-scale small samples

We present a home-built scanning tunneling microscope (STM) which allows us to precisely position the tip on any specified small sample or sample feature of micron scale. The core structure is a stand-alone soft junction mechanical loop (SJML), in which a small piezoelectric tube scanner is mounted on a sliding piece and a "U"-like soft spring strip has its one end fixed to the sliding piece and its opposite end holding the tip pointing to the sample on the scanner. Here, the tip can be precisely aligned to a specified small sample of micron scale by adjusting the position of the spring-clamped sample on the scanner in the field of view of an optical microscope. The aligned SJML can be transferred to a piezoelectric inertial motor for coarse approach, during which the U-spring is pushed towards the sample, causing the tip to approach the pre-aligned small sample. We have successfully approached a hand cut tip that was made from 0.1 mm thin Pt∕Ir wire to an isolated individual 32.5 × 32.5 μm(2) graphite flake. Good atomic resolution images and high quality tunneling current spectra for that specified tiny flake are obtained in ambient conditions with high repeatability within one month showing high and long term stability of the new STM structure. In addition, frequency spectra of the tunneling current signals do not show outstanding tip mount related resonant frequency (low frequency), which further confirms the stability of the STM structure.

18/20 T high magnetic field scanning tunneling microscope with fully low voltage operability, high current resolution, and large scale searching ability

We present a home-built 18/20 T high magnetic field scanning tunneling microscope (STM) featuring fully low voltage (lower than ±15 V) operability in low temperatures, large scale searching ability, and 20 fA high current resolution (measured by using a 100 GOhm dummy resistor to replace the tip-sample junction) with a bandwidth of 3.03 kHz. To accomplish low voltage operation which is important in achieving high precision, low noise, and low interference with the strong magnetic field, the coarse approach is implemented with an inertial slider driven by the lateral bending of a piezoelectric scanner tube (PST) whose inner electrode is axially split into two for enhanced bending per volt. The PST can also drive the same sliding piece to inertial slide in the other bending direction (along the sample surface) of the PST, which realizes the large area searching ability. The STM head is housed in a three segment tubular chamber, which is detachable near the STM head for the convenience of sample and tip changes. Atomic resolution images of a graphite sample taken under 17.6 T and 18.0001 T are presented to show its performance.

Ultra compact multitip scanning tunneling microscope with a diameter of 50 mm

We present a multitip scanning tunneling microscope (STM) where four independent STM units are integrated on a diameter of 50 mm. The coarse positioning of the tips is done under the control of an optical microscope or scanning electron microscopy in vacuum. The heart of this STM is a new type of piezoelectric coarse approach called KoalaDrive. The compactness of the KoalaDrive allows building a four-tip STM as small as a single-tip STM with a drift of less than 0.2 nm/min at room temperature and lowest resonance frequencies of 2.5 kHz (xy) and 5.5 kHz (z). We present as examples of the performance of the multitip STM four point measurements of silicide nanowires and graphene.

Deformable Registration of the Inflated and Deflated Lung for Cone-Beam CT-Guided Thoracic Surgery.

Intraoperative cone-beam CT (CBCT) could offer an important advance to thoracic surgeons in directly localizing subpalpable nodules during surgery. An image-guidance system is under development using mobile C-arm CBCT to directly localize tumors in the OR, potentially reducing the cost and logistical burden of conventional preoperative localization and facilitating safer surgery by visualizing critical structures surrounding the surgical target (e.g., pulmonary artery, airways, etc.). To utilize the wealth of preoperative image/planning data and to guide targeting under conditions in which the tumor may not be directly visualized, a deformable registration approach has been developed that geometrically resolves images of the inflated (i.e., inhale or exhale) and deflated states of the lung. This novel technique employs a coarse model-driven approach using lung surface and bronchial airways for fast registration, followed by an image-driven registration using a variant of the Demons algorithm to improve target localization to within ∼1 mm. Two approaches to model-driven registration are presented and compared - the first involving point correspondences on the surface of the deflated and inflated lung and the second a mesh evolution approach. Intensity variations (i.e., higher image intensity in the deflated lung) due to expulsion of air from the lungs are accounted for using an a priori lung density modification, and its improvement on the performance of the intensity-driven Demons algorithm is demonstrated. Preliminary results of the combined model-driven and intensity-driven registration process demonstrate accuracy consistent with requirements in minimally invasive thoracic surgery in both target localization and critical structure avoidance.

A nanopositioner for scanning probe microscopy: The KoalaDrive

We present a new type of piezoelectric nanopositioner called KoalaDrive which can have a diameter less than 2.5 mm and a length smaller than 10 mm. The new operating principle provides a smooth travel sequence and avoids shaking which is intrinsic to nanopositioners based on inertial motion with sawtooth driving signals. In scanning probe microscopy, the KoalaDrive can be used for the coarse approach of the tip or sensor towards the sample. Inserting the KoalaDrive in a piezo tube for xyz-scanning integrates a complete scanning tunneling microscope (STM) inside a 4 mm outer diameter piezo tube of <10 mm length. The use of the KoalaDrive makes the scanning probe microscopy design ultracompact and accordingly leads to a high mechanical stability. The drive is UHV, low temperature, and magnetic field compatible. The compactness of the KoalaDrive allows building a multi-tip STM as small as a single tip STM.

A molecular dynamics implementation of the 3D Mercedes-Benz water model

The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution. Program summary Program title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water) Catalogue identifier: AEKM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 20 501 No. of bytes in distributed program, including test data, etc.: 551 044 Distribution format: tar.gz Programming language: Fortran 90 Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer. Operating system: Linux, Unix, OS X Has the code been vectorized or parallelized?: The code has been parallelized using MPI. RAM: Depends on size of system, about 5 MB for 1500 molecules. Classification: 7.7 External routines: A random number generator, Mersenne Twister ( http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution. Nature of problem: Molecular dynamics simulation of a new geometric water model. Solution method: New force-field for water molecules, velocity–Verlet integration, representation of molecules as rigid particles with rotations described using quaternion algebra. Restrictions: Memory and cpu time limit the size of simulations. Additional comments: Software web site: https://gitorious.org/cashew/. Running time: Depends on the size of system. The sample tests provided only take a few seconds.