Search results for "Simulation."

Equilibrium coverage fluctuations: a new approach to quantify reversible adsorption of proteins.

2005

First-principles simulations of hydrogen peroxide formation catalyzed by small neutral gold clusters.

2009

Energetics and dynamical pathways for hydrogen peroxide formation from H(2) and O(2) bound to neutral gold dimers and tetramers have been investigated by applying several strategies: T = 0 K geometry optimizations, constrained Car-Parrinello molecular dynamics simulations at T = 300 K and metadynamics at T = 300 K. The competing reaction channels for water and hydrogen peroxide formation have been found and characterized. In each case, the reaction barriers for Au cluster catalyzed proton transfer are less than 1 eV. Water formation is a competitive reaction channel, and the relative weight of H(2)O and H(2)O(2) products may depend on the chosen Au cluster size. Dynamic simulations demonstr…

Global retention models and their application to the prediction of chromatographic fingerprints

2020

Abstract The resolution of samples containing unknown compounds of different nature, or without standards available, as is the case of chromatographic fingerprints, is still a challenge. Possibly, the most problematic aspect that prevents systematic method development is finding models that describe without bias the retention behaviour of the compounds in the samples. In this work, the use of global models (able to describe the whole sample) is proposed as an alternative to the use of individual models for each solute. Global models contain parameters that are specific for each solute, while other parameters ‒related to the column and solvent‒ are common for all solutes. A special regressio…

Scrutiny of annexin A1 mediated membrane-membrane interaction by means of a thickness shear mode resonator and computer simulations.

2004

The dissipational quartz crystal microbalance (D-QCM) technology was applied to monitor the adsorption of vesicles to membrane-bound annexin A1 by simultaneously reading out the shifts in resonance frequency and dissipation. Solid-supported membranes (SSMs) composed of a chemisorbed octanethiol monolayer and a physisorbed 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine monolayer were immobilized on the gold electrode of a 5 MHz quartz plate. Adsorption and desorption of annexin A1 to the SSM was followed by means of the QCM technique. After nonbound annexin A1 was removed from solution, the second membrane binding was monitored by the D-QCM t…

Partially Reversible Adsorption of Annexin A1 on POPC/POPS Bilayers Investigated by QCM Measurements, SFM, and DMC Simulations

2005

The kinetics of annexin A1 binding to solid-supported lipid bilayers consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS; 4:1) has been investigated as a function of the calcium ion concentration in the bulk phase. Quartz crystal microbalance measurements in conjunction with scanning force microscopy, fluorescence microscopy, and computer simulations indicate that at a given Ca2+ concentration annexin A1 adsorbs irreversibly on membrane domains enriched in POPS. By contrast, annexin A1 adsorbs reversibly on the POPC-enriched phase, which is composed of single POPS molecules embedded within a POPC matrix. The overall are…

Robust dynamical pattern formation from a multifunctional minimal genetic circuit.

2010

Abstract Background A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory networks play an important role in shaping the development of multicellular organisms, whereas oscillatory circuits are used to control gene expression under variable environments such as the light-dark cycle. Results We propose a new mechanism to generate developmental patterns and oscillations using a minimal number of genes. For this, we design a synthetic gene circuit with an antagonistic self-regulation to study the spatio-temporal control of protein expression. He…

Analysing the Spanish smoke-free legislation of 2006: a new method to quantify its impact using a dynamic model.

2011

Background: There are many models that study aspects of smoking habits: the influence of price, tax, relapse time, and the effects of prohibition. There are also studies examining the effects of the Spanish smoke-free law. We wanted to build a model able to separate the effect of the law from the pre-law evolution of smoking habits. Methods: Using data from the Spanish Ministry of Health and Social Policy, we developed a dynamic model of tobacco use. The model projects the evolution over time of the number of non-smokers, smokers and ex-smokers before 2006. Then, we compared the predictions of the model with data for the years after the law came into force, 2006 and 2009. Results: We show t…

Analytically solvable Hamiltonians for quantum two-level systems and their dynamics

2014

A simple systematic way of obtaining analytically solvable Hamiltonians for quantum two-level systems is presented. In this method, a time-dependent Hamiltonian and the resulting unitary evolution operator are connected through an arbitrary function of time, furnishing us with new analytically solvable cases. The method is surprisingly simple, direct, and transparent and is applicable to a wide class of two-level Hamiltonians with no involved constraint on the input function. A few examples illustrate how the method leads to simple solvable Hamiltonians and dynamics.

Variational formulations and extra boundary conditions within stress gradient elasticity theory with extensions to beam and plate models

2016

Abstract The principle of minimum total potential energy and the primary principle of virtual power for stress gradient elasticity are presented as kinematic type constructs dual of analogous static type principles from the literature (Polizzotto, 2014; Polizzotto, 2015a). The extra gradient-induced boundary conditions are formulated as “boundary congruence conditions” on the microstructure’s deformation relative to the continuum, which ultimately require that the normal derivative of the stresses must vanish at the boundary surface. Two forms of the governing PDEs for the relevant boundary-value problem are presented and their computational aspects are discussed. The Timoshenko beam and th…

Intrusion of nonwetting liquid in paper

2007

The saturation curve of a sample of paper board was measured with mercury-intrusion porosimetry, and the three-dimensional structure of its pore space was determined by x-ray tomographic imaging. Ab initio numerical simulation of intrusion on the tomographic reconstruction, based on the lattice-Boltzmann method, was in excellent agreement with the measured saturation curve. A numerical invasion-percolation simulation in the same tomographic reconstruction showed good agreement with the lattice-Boltzmann simulation. The access function of the sample, determined from the saturation curve and the pore-throat distribution determined from the tomographic reconstruction, indicated that the ink-bo…