Search results for " Simulation"
showing 10 items of 4034 documents
Blocking of an ion channel by a highly charged drug: Modeling the effects of applied voltage, electrolyte concentration, and drug concentration
2005
We present a simple physical model to estimate the blocked pore probability of an ion channel that can be blocked by a highly charged drug in solution. The model is inspired by recent experimental work on the blocking of the ${\mathrm{PA}}_{63}$ channel, involved in the anthrax toxin infection, by a highly charged drug [Karginov et al. PNAS 102, 15075 (2005)]. The drug binding to the pore is highly specific but the strong dependence of blocking on the applied voltage and electrolyte concentration suggests that long range electrostatic interactions are important. Since basic electrostatic concepts rather than detailed molecular models are considered, the microscopic details of the channel bl…
SELF SIMILARITY IN SWELLING SYSTEMS: FRACTAL PROPERTIES OF PEAT
1994
Sphagnum peat gives an example of a swelling system with a self-similar structure in sufficiently wide range of scales. The surface fractal dimension, dfs, has been calculated by means of thermodynamic method on the basis of water adsorption and capillary equilibrium measurements. This method makes possible the exploration of the self-similarity in the scale range over at least 4 decimal orders of magnitude from 1 nm to 10 μm. In a sample explored, two ranges of fractality have been observed: dfs ≈ 2.55 in the range 1.5–80 nm and dfs ≈ 2.42 in the range 0.25–9 µm.
Nanoparticles Size Distribution Assessment During Early Synthesis Stages
2021
Nanotechnology, an innovative field of material science, designs and produces nanostructures materials with unique properties that make them suited for various bioengineering applications. The shape and the dimension are the main variables depending on the method of synthesis or chemical precursors. Silver nanoparticles obtained through chemical synthesis exhibit as strong antibacterial effect if their size lays in a well-defined range. However, a small size of such particles, in the range of nanometers to several tens of nanometers, requires specific techniques as Dynamic Light Scattering or Transmission Electron Microscopy, both being affected by certain assumptions or by the high cost an…
A new method to evaluate the influence of the glenosphere positioning on stability and range of motion of a reverse shoulder prosthesis
2019
Abstract Purpose Shoulder instability and reduced range of motion are two common complications of a total reverse shoulder arthroplasty. In this work, a new approach is proposed to estimate how the glenoid component positioning can influence the stability and the range of motion of a reverse shoulder prosthesis. Materials and methods A standard reverse shoulder prosthesis has been analysed. To perform virtual simulation of the shoulder-prosthesis assembly, all the components of the prosthesis have been acquired via a 3D laser scanner and the solid models of the shoulder bones have been reconstructed through CT images. Loads on the shoulder joint have been estimated using anatomical models d…
Time and work generalised precedence relationships in project scheduling with pre-emption: An application to the management of Service Centres
2012
Abstract In this paper we present an application of project scheduling concepts and solution procedures for the solution of a complex problem that comes up in the daily management of many company Service Centres. The real problem has been modelled as a multi-mode resource-constrained project scheduling problem with pre-emption, time and work generalised precedence relationships with minimal and maximal time lags between the tasks and due dates. We present a complete study of work GPRs which includes proper definitions, a new notation and all possible conversions amongst them. Computational results that show the efficiency of the proposed hybrid genetic algorithm and the advantages of allowi…
Mechanism change in a simulation of peer review: from junk support to elitism
2014
Abstract Peer review works as the hinge of the scientific process, mediating between research and the awareness/acceptance of its results. While it might seem obvious that science would regulate itself scientifically, the consensus on peer review is eroding; a deeper understanding of its workings and potential alternatives is sorely needed. Employing a theoretical approach supported by agent-based simulation, we examined computational models of peer review, performing what we propose to call redesign, that is, the replication of simulations using different mechanisms. Here, we show that we are able to obtain the high sensitivity to rational cheating that is present in literature. In additio…
A Rayleigh-Ritz approach for postbuckling analysis of variable angle tow composite stiffened panels
2018
Abstract A Rayleigh-Ritz solution approach for generally restrained multilayered variable angle tow stiffened plates in postbuckling regime is presented. The plate model is based on the first order shear deformation theory and accounts for geometrical nonlinearity through the von Karman’s assumptions. Stiffened plates are modelled as assembly of plate-like elements and penalty techniques are used to join the elements in the assembled structure and to apply the kinematical boundary conditions. General symmetric and unsymmetric stacking sequences are considered and Legendre orthogonal polynomials are employed to build the trial functions. A computer code was developed to implement the propose…
Unveiling the reaction mechanism of novel copper N-alkylated tetra-azacyclophanes with outstanding superoxide dismutase activity.
2020
Quantum chemical and multiscale calculations reveal the mechanistic pathway of two superoxide dismutase mimetic N-alkylated tetra-azacyclophane copper complexes with remarkable activity. The arrangement of the binding site afforded by the bulky alkyl substituents and the coordinated water molecule as a proton source play key roles in the reaction mechanism.
Computational simulations on the binding and reactivity of a nitrile inhibitor of the SARS-CoV-2 main protease.
2021
We present a detailed computational analysis of the binding mode and reactivity of the novel oral inhibitor PF-07321332 developed against the SARS-CoV-2 3CL protease. Alchemical free energy calculations suggest that positions P3 and P4 could be susceptible to improvement in order to get a larger binding strength. QM/MM simulations unveil the reaction mechanism for covalent inhibition, showing that the nitrile warhead facilitates the recruitment of a water molecule for the proton transfer step.
Dynamics and reactivity in Thermus aquaticus N6-adenine methyltransferase.
2014
M.TaqI is a DNA methyltransferase from Thermus aquaticus that catalyzes the transfer of a methyl group from S-adenosyl-l-methionine to the N6 position of an adenine, a process described only in prokaryotes. We have used full atomistic classical molecular dynamics simulations to explore the protein–SAM–DNA ternary complex where the target adenine is flipped out into the active site. Key protein–DNA interactions established by the target adenine in the active site are described in detail. The relaxed structure was used for a combined quantum mechanics/molecular mechanics exploration of the reaction mechanism using the string method. According to our free energy calculations the reaction takes…