Search results for "Method"

Monte carlo studies of phase transitions in polymer blends and block copolymer melts

1994

The unmixing transition of both symmetrical polymer blends AB (i.e. chain lengthsNA=NB=N) and asymmetrical ones (NB/NA=2,3) is studied by large-scale Monte Carlo simulations of the bond fluctuation model. Combination of semi-grand-canonical simulation techniques, «histogram reweighting» and finitesize scaling allows an accurate location of the coexistence curve in the critical region. The variation of the critical temperature with chain length (N) is studied and compared to theoretical predictions. For the symmetrical case, use of chain lengths up toN=512 allows a rough estimation of crossover scaling functions for the crossover from Ising to mean-field exponents. The order-disorder transit…

Liquid-vapour phase behaviour of a symmetrical binary fluid mixture

1998

Using Monte-Carlo simulation and mean field calculations, we study the liquid-vapour phase diagram of a square well binary fluid mixture as a function of a parameter $\delta$ measuring the relative strength of interactions between particles of dissimilar and similar species. The results reveal a rich variety of liquid-vapour coexistence behaviour as $\delta$ is tuned. Specifically, we uncover critical end point behaviour, a triple point involving a vapour and two liquids of different density, and tricritical behaviour. For a certain range of $\delta$, the mean field calculations also predict a `hidden' (metastable) liquid-vapour binodal.

The droplet evaporation/condensation transition in a finite volume

2003

A fluid in the NVT ensemble at T less than the critical temperature T_c and rho = N/V somewhat in excess of rho_coex (density of the saturated gas in the gas-liquid transition) is considered. For V->infinity, a macroscopic liquid droplet coexists with surrounding saturated gas according to the lever rule. For finite V, droplets can only exist if they exceed a minimum size. A (rounded) first order transition of the system occurs when the droplet evaporates into the supersaturated gas.Simulation evidence for this transition is given for a Lennard-Jones model and interpreted by a phenomenological theory. At the transition, the chemical potential difference mu_t-mu_coex scales like L^(-d/(d+…

Efficient prediction of thermodynamic properties of quadrupolar fluids from simulation of a coarse-grained model: the case of carbon dioxide.

2008

Monte Carlo simulations are presented for a coarse-grained model of real quadrupolar fluids. Molecules are represented by particles interacting with Lennard-Jones forces plus the thermally averaged quadrupole-quadrupole interaction. The properties discussed include the vapor-liquid coexistence curve, the vapor pressure along coexistence, and the surface tension. The full isotherms are also accessible over a wide range of temperatures and densities. It is shown that the critical parameters (critical temperature, density, and pressure) depend almost linearly on a quadrupolar parameter q=Q(*4)T*, where Q* is the reduced quadrupole moment of the molecule and T* the reduced temperature. The mode…

A hydrodynamic water quality model for propagation of pollutants in rivers.

2010

Numerical modelling can be a useful tool to assess a receiving water body's quality state. Indeed, the use of mathematical models in river water quality management has become a common practice to show the cause-effect relationship between emissions and water body quality and to design as well as assess the effectiveness of mitigation measures. In the present study, a hydrodynamic river water quality model is presented. The model consists of a quantity and a quality sub-model. The quantity sub-model is based on the Saint Venant equations. The solution of the Saint Venant equations is obtained by means of an explicit scheme based on space-time conservation. The method considers the unificatio…

Multiscale modeling on biological systems

2018

MicroRNA Interaction Networks

2021

La tesi di Giorgio Bertolazzi è incentrata sullo sviluppo di nuovi algoritmi per la predizione dei legami miRNA-mRNA. In particolare, un algoritmo di machine-learning viene proposto per l'upgrade del web tool ComiR; la versione originale di ComiR considerava soltanto i siti di legame dei miRNA collocati nella regione 3'UTR dell'RNA messaggero. La nuova versione di ComiR include nella ricerca dei legami la regione codificante dell'RNA messaggero. Bertolazzi’s thesis focuses on developing and applying computational methods to predict microRNA binding sites located on messenger RNA molecules. MicroRNAs (miRNAs) regulate gene expression by binding target messenger RNA molecules (mRNAs). Therefo…

Fast comparison of DNA sequences by oligonucleotide profiling

2008

Provisional abstact and full-text PDF files correspond to the article as it appeared upon acceptance. Fully formatted PDF and final abstract will be made available soon.

Electronic aspects of the hydride transfer mechanism. Ab initio analytical gradient studies of the cyclopropenyl‐cation/lithium hydride model reactan…

1985

The electronic mechanisms of a model hydride transfer reaction are theoretically studied with ab inito RHF and UHF SCF MO procedures at the 4‐31G basis set level and analytical gradient methods. The model system describes the reduction of cyclopropenyl cation to cyclopropene by the oxidation of lithium hydride to lithium cation. The molecular fragments corresponding to the asymptotic reactive channels characterizing the stepwise mechanisms currently discussed in the literature have been characterized. The binding energy between the fragments is estimated within a simple electrostatic approximate scheme. The results show that a hydride‐ion mechanism is a likely pathway for this particular sy…

Protein Interaction Networks and Disease: Highlights of the 3rd Challenges in Computational Biology Meeting

2017

Cellular functions are managed by a complex network of protein interactions, the malfunction of which may derive in disease phenotypes. In spite of the incompleteness and noise present in our current protein interaction maps, computational biologists are making strenuous efforts to extract knowledge from these intricate networks and, through their integration with other types of biological data, expedite the development of novel and more effective treatments against human disorders. The 3rd Challenges in Computational Biology meeting revolved around the Protein Interaction Networks and Disease subject, bringing expert network biologists to the city of Mainz, Germany to debate the current st…