Search results for " Simulation"
showing 10 items of 4034 documents
Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations.
2017
We performed quantum-chemical calculations, ab initio molecular dynamics, hybrid quantum mechanics/molecular mechanics (QM/MM) and enhanced sampling metadynamics simulations to investigate the origin of metal specificity in isatin hydrolase from Labrenzia aggregata. The peculiar octahedral binding geometry of the Mn2+ ion in the Michaelis complex includes both the isatin substrate and the catalytic water within the first coordination shell of the cation. Our calculations show that the same arrangement of the ligands cannot be efficiently achieved in the presence of other small divalent metal cations such as Zn2+ or Cu2+ . On the contrary, bulkier alkaline-earth cations such as Mg2+ , which …
Nitrated Fatty Acids Modulate the Physical Properties of Model Membranes and the Structure of Transmembrane Proteins
2017
Nitrated fatty acids (NO2 -FAs) act as anti-inflammatory signal mediators, albeit the molecular mechanisms behind NO2 -FAs' influence on diverse metabolic and signaling pathways in inflamed tissues are essentially elusive. Here, we combine fluorescence measurements with surface-specific sum frequency generation vibrational spectroscopy and coarse-grained computer simulations to demonstrate that NO2 -FAs alter lipid organization by accumulation at the membrane-water interface. As the function of membrane proteins strongly depends on both, protein structure as well as membrane properties, we consecutively follow the structural dynamics of an integral membrane protein in presence of NO2 -FAs. …
EPR/ALANINE PELLETS WITH LOW Gd CONTENT FOR NEUTRON DOSIMETRY
2013
This paper reports on results obtained by electron paramagnetic resonance (EPR) measurements and Monte Carlo (MC) simulation on a blend of alanine added with low content of gadolinium oxide (5 % by weight) to improve the sensitivity to thermal neutron without excessively affecting tissue equivalence. The sensitivity is enhanced by this doping procedure of more an order of magnitude. The results are compared with those obtained with the addition of boric acid (50 % by weight) where boron is in its natural isotopic composition in order to produce low-cost EPR dosemeters. The gadolinium addition influences neutron sensitivity more than the boron addition. The presence of additives does not sub…
Adsorption and desorption surface dynamics of gaseous adsorbate on silicate-1 by molecular dynamics simulation
2013
The dynamics of adsorption and desorption of gaseous molecules on the external surface of a crystal and a membrane of zeolite silicate-1 is investigated by molecular dynamics simulation. The gases ...
Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectr…
2014
In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein + hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin + hydration …
ON SOME GENERALIZATION OF SMOOTHING PROBLEMS
2015
The paper deals with the generalized smoothing problem in abstract Hilbert spaces. This generalized problem involves particular cases such as the interpolating problem, the smoothing problem with weights, the smoothing problem with obstacles, the problem on splines in convex sets and others. The theorem on the existence and characterization of a solution of the generalized problem is proved. It is shown how the theorem gives already known theorems in special cases as well as some new results.
Pressure-Induced Deformation of Pillar-Type Profiled Membranes and Its Effects on Flow and Mass Transfer
2019
In electro-membrane processes, a pressure difference may arise between solutions flowing in alternate channels. This transmembrane pressure (TMP) causes a deformation of the membranes and of the fluid compartments. This, in turn, affects pressure losses and mass transfer rates with respect to undeformed conditions and may result in uneven flow rate and mass flux distributions. These phenomena were analyzed here for round pillar-type profiled membranes by integrated mechanical and fluid dynamics simulations. The analysis involved three steps: (1) A conservatively large value of TMP was imposed, and mechanical simulations were performed to identify the geometry with the minimum pillar density…
The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization.
2022
Photoactivation of bacteriophytochrome involves a cis–trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the c…
ASPECTS REGARDING THE OPTIMIZATION OF THE QUALITY OF MANAGERIAL DECISIONS - SOLVING AN OPTIMIZATION PROBLEM IN THE SENSE OF SUSTAINABILITY WITH WINQSB
2012
In this paper we present an optimization problem solving, problem that is mathematically shaped as a linear programming problem. This is made with the purpose of finding an optimal solution which is also a sustainable one. In the present and future society, it is clear that nothing can be done honestly, but only in the sense of a professional and sustainable thinking (Konrad, C., 2011, pp.202-217, Petrescu, I., 2006, p.1). To think sustainable can also mean “to be calculated”, in popular language “to choose wisely”, all for achieving the proposed project, being careful to using non-renewable resources, to pollution, to protection for human resource, etc. Of course that the logical and preci…
APPLYING PERT AND CRITICAL PATH METHOD IN HUMAN RESOURCE TRAINING
2011
The subject of the article is referring to the modelling and simulating of the formation of human resources by applying the PERT/CPM (Program Evaluation and Review Technique/Critical Path Method) and the taking into consideration of some risks associated to this activity. The aim of the article is to offer practical support to the management of organizations in order to make a formation program of human resources, which implies activities of precedence and interrelated, critical paths, the distribution of time resources and necessary costs for the fulfilment of the organizational objectives.