SRIM is a software package concerning the S topping and R ange of I ons in M atter. Since its introduction in 1985, major upgrades are made about every six years. Currently, more than 700 scientific citations are made to SRIM every year. For SRIM-2010 , the following major improvements have been made: (1) About 2800 new experimental stopping powers were added to the database, increasing it to over 28,000 stopping values. (2) Improved corrections were made for the stopping of ions in compounds. (3) New heavy ion stopping calculations have led to significant improvements on SRIM stopping accuracy. (4) A self-contained SRIM module has been included to allow SRIM stopping and range values to be controlled and read by other software applications. (5) Individual interatomic potentials have been included for all ion/atom collisions, and these potentials are now included in the SRIM package. A full catalog of stopping power plots can be downloaded at www.SRIM.org . Over 500 plots show the accuracy of the stopping and ranges produced by SRIM along with 27,000 experimental data points. References to the citations which reported the experimental data are included.

SRIM – The stopping and range of ions in matter (2010)

Ion acceleration driven by superintense laser pulses is attracting an impressive and steadily increasing effort. Motivations can be found in the applicative potential and in the perspective to investigate novel regimes as available laser intensities will be increasing. Experiments have demonstrated, over a wide range of laser and target parameters, the generation of multi-MeV proton and ion beams with unique properties such as ultrashort duration, high brilliance, and low emittance. An overview is given of the state of the art of ion acceleration by laser pulses as well as an outlook on its future development and perspectives. The main features observed in the experiments, the observed scaling with laser and plasma parameters, and the main models used both to interpret experimental data and to suggest new research directions are described.

/pdf/ion-acceleration-by-superintense-laser-plasma-interaction-2jqzeizem7.pdf

Ion acceleration by superintense laser-plasma interaction

The SRIM (formerly TRIM) Monte Carlo simulation code is widely used to compute a number of parameters relevant to ion beam implantation and ion beam processing of materials. It also has the capability to compute a common radiation damage exposure unit known as atomic displacements per atom (dpa). Since dpa is a standard measure of primary radiation damage production, most researchers who employ ion beams as a tool for inducing radiation damage in materials use SRIM to determine the dpa associated with their irradiations. The use of SRIM for this purpose has been evaluated and comparisons have been made with an internationally-recognized standard definition of dpa, as well as more detailed atomistic simulations of atomic displacement cascades. Differences between the standard and SRIM-based dpa are discussed and recommendations for future usage of SRIM in radiation damage studies are made. In particular, it is recommended that when direct comparisons between ion and neutron data are intended, the Kinchin–Pease option of SRIM should be selected.

On the use of SRIM for computing radiation damage exposure

Objective To review and synthesize information concerning the pathogenesis ofage-related macular degeneration (AMD). Methods Review of the English-language literature. Results Five concepts relevant to the cell biology of AMD are as follows: (1)AMD involves aging changes plus additional pathological changes (ie, AMD isnot just an aging change); (2) in aging and AMD, oxidative stress causes retinalpigment epithelial (RPE) and, possibly, choriocapillaris injury; (3) in AMD(and perhaps in aging), RPE and, possibly, choriocapillaris injury resultsin a chronic inflammatory response within the Bruch membrane and the choroid;(4) in AMD, RPE and, possibly, choriocapillaris injury and inflammation leadto formation of an abnormal extracellular matrix (ECM), which causes altereddiffusion of nutrients to the retina and RPE, possibly precipitating furtherRPE and retinal damage; and (5) the abnormal ECM results in altered RPE-choriocapillarisbehavior leading ultimately to atrophy of the retina, RPE, and choriocapillarisand/or choroidal new vessel growth. In this sequence of events, both the environmentand multiple genes can alter a patient's susceptibility to AMD. Implicit inthis characterization of AMD pathogenesis is the concept that there is linearprogression from one stage of the disease to the next. This assumption maybe incorrect, and different biochemical pathways leading to geographic atrophyand/or choroidal new vessels may operate simultaneously. Conclusions Better knowledge of AMD cell biology will lead to better treatmentsfor AMD at all stages of the disease. Many unanswered questions regardingAMD pathogenesis remain. Multiple animal models and in vitro models of specificaspects of AMD are needed to make rapid progress in developing effective therapiesfor different stages of the disease.

https://jamanetwork.com/journals/jamaophthalmology/articlepdf/416250/EMO20000.pdf

Current Concepts in the Pathogenesis of Age-Related Macular Degeneration

Age-related macular degeneration: etiology, pathogenesis, and therapeutic strategies.

/pdf/srim-the-stopping-and-range-of-ions-in-matter-1uyqpxujhc.pdf

SRIM : the stopping and range of ions in matter

Spinal Wistar Hannover rats trained to step bipedally on a treadmill with manual assistance of the hindlimbs have been shown to improve their stepping ability. Given the improvement in motor performance with practice and the ability of the spinal cord circuitry to learn to step more effectively when the mode of training allows variability, we examined why this intrinsic variability is an important factor. Intramuscular EMG electrodes were implanted to monitor and compare the patterns of activation of flexor (tibialis anterior) and extensor (soleus) muscles associated with a fixed-trajectory and assist-as-needed (AAN) step training paradigms in rats after a complete midthoracic (T8-T9) spinal cord transection. Both methods involved a robotic arm attached to each ankle of the rat to provide guidance during stepping. The fixed trajectory allowed little variance between steps, and the AAN provided guidance only when the ankle deviated a specified distance from the programmed trajectory. We hypothesized that an AAN paradigm would impose fewer disruptions of the control strategies intrinsic to the spinal locomotor circuitry compared with a fixed trajectory. Intrathecal injections of quipazine were given to each rat to facilitate stepping. Analysis confirmed that there were more corrections within a fixed-trajectory step cycle and consequently there was less coactivation of agonist and antagonist muscles during the AAN paradigm. These data suggest that some critical level of variation in the specific circuitry activated and the resulting kinematics reflect a fundamental feature of the neural control mechanisms even in a highly repetitive motor task.

https://www.jneurosci.org/content/jneuro/30/32/10720.full.pdf

Why Variability Facilitates Spinal Learning

Skill acquisition requires distributed learning both within (online) and across (offline) days to consolidate experiences into newly learned abilities. In particular, piloting an aircraft requires skills developed from extensive training and practice. Here, we tested the hypothesis that transcranial direct current stimulation (tDCS) can modulate neuronal function to improve skill learning and performance during flight simulator training of aircraft landing procedures. Thirty-two right-handed participants consented to participate in four consecutive daily sessions of flight simulation training and received sham or anodal high-definition-tDCS to the right dorsolateral prefrontal cortex (DLPFC) or left motor cortex (M1) in a randomized, double-blind experiment. Continuous electroencephalography (EEG) and functional near infrared spectroscopy (fNIRS) were collected during flight simulation, n-back working memory, and resting-state assessments. tDCS of the right DLPFC increased midline-frontal theta-band activity in flight and n-back working memory training, confirming tDCS-related modulation of brain processes involved in executive function. This modulation corresponded to a significantly different online and offline learning rates for working memory accuracy and decreased inter-subject behavioral variability in flight and n-back tasks in the DLPFC stimulation group. Additionally, tDCS of left M1 increased parietal alpha power during flight tasks and tDCS to the right DLPFC increased midline frontal theta-band power during n-back and flight tasks. These results demonstrate a modulation of group variance in skill acquisition through an increasing in learned skill consistency in cognitive and real-world tasks with tDCS. Further, tDCS performance improvements corresponded to changes in electrophysiological and blood-oxygenation activity of the DLPFC and motor cortices, providing a stronger link between modulated neuronal function and behavior.

/pdf/transcranial-direct-current-stimulation-modulates-neuronal-2gygswuz2j.pdf

Transcranial Direct Current Stimulation Modulates Neuronal Activity and Learning in Pilot Training.

By the end of 2002, 33 398 patients worldwide had been treated with proton radiotherapy, 10 829 for eye diseases. The dose prediction algorithms used today for ocular proton therapy treatment planning rely on parameterizations of measured proton dose distributions, i.e., broad-beam and pencil-beam techniques, whose predictive capabilities are inherently limited by severe approximations and simplifications in modelling the radiation transport physics. In contrast, the Monte Carlo radiation transport technique can, in principle, provide accurate predictions of the proton treatment beams by taking into account all the physical processes involved, including coulombic energy loss, energy straggling, multiple Coulomb scattering, elastic and nonelastic nuclear interactions, and the transport of secondary particles. It has not been shown, however, whether it is possible to commission a proton treatment planning system by using data exclusively from Monte Carlo simulations of the treatment apparatus and a phantom. In this work, we made benchmark comparisons between Monte Carlo predictions and measurements of an ocular proton treatment beamline. The maximum differences between absorbed dose profiles from simulations and measurements were 6% and 0.6 mm, while typical differences were less than 2% and 0.2 mm. The computation time for the entire virtual commissioning process is less than one day. The study revealed that, after a significant development effort, a Monte Carlo model of a proton therapy apparatus is sufficiently accurate and fast for commissioning a treatment planning system.

https://iopscience.iop.org/article/10.1088/0031-9155/50/22/002/pdf

Matthias Ziegler

Papers

SRIM – The stopping and range of ions in matter (2010)

SRIM : the stopping and range of ions in matter

Why Variability Facilitates Spinal Learning

Transcranial Direct Current Stimulation Modulates Neuronal Activity and Learning in Pilot Training.

Monte Carlo simulations of a nozzle for the treatment of ocular tumours with high-energy proton beams