Search results for "simulations"
showing 10 items of 288 documents
Best Practices in Constant pH MD Simulations: Accuracy and Sampling
2022
Various approaches have been proposed to include the effect of pH in molecular dynamics (MD) simulations. Among these, the λ-dynamics approach proposed by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414−2423] can be performed with little computational overhead and hfor each typeence be used to routinely perform MD simulations at microsecond time scales, as shown in the accompanying paper [Aho, N. et al. J. Chem. Theory Comput.2022, DOI: 10.1021/acs.jctc.2c00516]. At such time scales, however, the accuracy of the molecular mechanics force field and the parametrization becomes critical. Here, we address these issues and provide the community with guidelines on…
New Capabilities of the FLUKA Multi-Purpose Code
2022
We would like to deeply thank the CERN Knowledge Transfer and Legal Service teams for their essential and extended support. Our appreciation also goes to the FLUKA.CERN Collaboration Board members for their strong commitment.
On the Finite Element Modeling of the Lumbar Spine: A Schematic Review
2023
Finite element modelling of the lumbar spine is a challenging problem. Lower back pain is among the most common pathologies in the global populations, owing to which the patient may need to undergo surgery. The latter may differ in nature and complexity because of spinal disease and patient contraindications (i.e., aging). Today, the understanding of spinal column biomechanics may lead to better comprehension of the disease progression as well as to the development of innovative therapeutic strategies. Better insight into the spine’s biomechanics would certainly guarantee an evolution of current device-based treatments. In this setting, the computational approach appears to be a remarkable …
Performance Enhancement of a Small Animal Positron Emission Tomograph based on Continuous Crystals and Silicon Photomultipliers
2017
La tomografía por emisión de positrones (PET, por sus siglas en inglés) es una técnica de Medicina Nuclear que permite obtener de manera no invasiva imágenes funcionales “in vivo” marcando un compuesto orgánico con un emisor de positrones. Los tomógrafos PET requieren un alta resolución espacial y sensibilidad para estimar con precisión la distribución del radiotrazador en el animal. Frente a los bloques pixelados comúnmente utilizados en PET, los detectores que consisten en la combinación de cristales continuos acoplados a fotodetectores segmentados pueden ofrecer una mayor eficiencia y una alta resolución espacial. Esta última depende de la precisión de los algoritmos de determinación de …
Highly-parallelized simulation of a pixelated LArTPC on a GPU
2023
The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The alg…
Multipoint transmission scheme for HSDPA
2013
Multiphoton Absorption of Myoglobin Nitric-Oxide complex: Relaxation by D-NEMD of a Stationary State
2012
ABSTRACT: The photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment …
Water effects on trehalose matrices studied through Molecular Dynamics
2012
Computer Simulations of the Band Structure and Density of States of the Linear Chains of NaCl Ions
2019
The authors thank Eugene Kotomin and V. Kuzovkov for fruitful discussions and valuable suggestions. A.I.P thanks A.Moskina for the technical assistance in preparation of the manuscript. A.I.P also gratefully acknowledges a project LZP-2018/1-0214 from the Latvian Council of Science for partial support.
Thermodynamics and kinetics of ion translocation in the human wild-type and E-1_A α7 nicotinic receptor
2021
We use an all-atom model of the human nicotinic acetylcholine receptor α7 in a conductive conformation, to provide the first available mapping of the potential of mean force for the ion translocation across the channel. The modeling is based on MD simulations combined with the milestoning method with Voronoi tessellation. The quality of the protein model and description is confirmed by the agreement with experimental data for proteins of the same family. The specific mutation E-1 ' A at the cytoplasmatic filter is here shown to strongly affect both sodium and chloride permeation, leading to a complete inversion of selectivity.