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Статті в журналах з теми "Simulazione molecolare"
Casino, Francesco G. "Principi di cinetica dei soluti in corso di aferesi terapeutica." Giornale di Clinica Nefrologica e Dialisi 25, no. 4_suppl (July 23, 2013): S9—S12. http://dx.doi.org/10.33393/gcnd.2013.1081.
Повний текст джерелаДисертації з теми "Simulazione molecolare"
Martini, Mara. "Simulazione delle proprietà morfologiche e strutturali di materiali biologici ed organici per dispositivi elettronici ed optoelettronici." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amslaurea.unibo.it/15555/.
Повний текст джерелаDal, Col Valentina. "In silico prediction of drug resistance: from cancer targeted therapy to cancer targeted prevention." Doctoral thesis, Università degli studi di Trieste, 2014. http://hdl.handle.net/10077/9976.
Повний текст джерелаLe recenti scoperte sulla natura dei processi genetici, implicati nelle trasformazioni neoplastiche, ci hanno permesso di identificare le principali lesioni cellulari che portano alla formazione del tumore, individuando in questo modo target selettivi sulla base dei quali progettare nuovi agenti terapeutici efficaci. La terapia bersaglio ha rappresentato una rivoluzione permettendo di superare l’aspecificità del trattamento antitumorale e colpendo, nello specifico, la causa biomolecolare del processo patologico neoplastico. I recenti sviluppi della modellistica molecolare si sono resi indispensabili per la ricerca oncologica. Questi, infatti, aprono delle opportunità per la scoperta di nuovi farmaci attraverso la comprensione delle basi molecolari delle malattie; si tratta di un metodo conveniente per identificare dei composti che siano in grado di bloccare l’azione di molte proteine, suggerite come fattori fondamentali in diversi tipi di neoplasie. In questo lavoro di tesi verrà adoperata un’ampia gamma di tecniche di simulazione molecolare al fine di studiare differenti problemi che possono comparire durante il trattamento chemioterapico. La scoperta di nuovi dettagli nei meccanismi che conducono alla carcinogenesi ha permesso di identificare proteine target innovative e più precise per affrontare la terapia senza effetti collaterali per le cellule sane. In particolare, saranno riportati in dettaglio gli studi che coinvolgono tre nuovi differenti target: il recettore σ1, la proteina -catenina e lo sviluppo di dendrimeri per una terapia di silenziamento genico. Tuttavia, nonostante i successi clinici della terapia bersaglio, molti pazienti che inizialmente hanno risposto positivamente manifestano una recidiva, come risultato di una resistenza acquisita; questo tipo di risposta può manifestarsi dopo un periodo variabile di trattamento cronico. L’approccio delle tecniche in silico può essere utilizzato per predire l’avvento di mutazioni secondarie attivanti e al contempo resistenti alla terapia e quindi aiutare nello sviluppo di una strategia di prevenzione focalizzata su una terapia multi-farmaco. In questo lavoro, verranno discusse in particolare delle mutazioni che coinvolgono i recettori c-Kit e Smoothened, pre e post trattamento. L’ampia serie di esempi illustrati e discussi qui enfatizza il ruolo e le potenzialità del modeling molecolare nello sviluppo della terapia bersaglio anti tumorale. Una valutazione in silico permette di prendere in considerazione la specificità molecolare del problema e ridurre drasticamente i tempi e i costi richiesti per formulare nuovi farmaci e strategie di intervento.
XXVI Ciclo
1986
Damuzzo, Martina <1986>. "Studio dell'inibizione dell'azione citolitica delle proteine NLP tramite simulazioni di screening virtuale e dinamica molecolare." Master's Degree Thesis, Università Ca' Foscari Venezia, 2019. http://hdl.handle.net/10579/15612.
Повний текст джерелаBRUSELLES, ALESSANDRO. "Studio delle proprietà strutturali e funzionali della dna topoisomerasi i umana attraverso simulazioni di dinamica molecolare classica." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2005. http://hdl.handle.net/2108/202639.
Повний текст джерелаHuman DNA topoisomerase I relaxes supercoiled DNA through the formation of a covalent intermediate in which the active-site tyrosine is transiently bound to the cleaved DNA strand. The structural and dynamical properties of various forms of this enzyme, both in complex with a 22bp DNA duplex and alone, have been investigated by Molecular Dynamics simulations. In detail, the simulations involved the following forms of the enzyme: the complexes DNA-topo58/6.3, DNA-topo70, DNA-topoT718A and the enzyme in the absence of DNA. The topo58/6.3 form of human topoisomerase I lacks the N-terminal and the linker domain while the topo70 form lacks only the N-terminal domain. The analyses on the DNA-topo58/6.3 complex showed a great number of correlated movements of core subdomain I and II residues, and a central role for helix 5 in the protein-DNA communication, in particular with the scissile strand downstream of the cleavage site. The comparison between topo70-DNA and topo58/6.3-DNA complexes Furthermore, the influence of the N-terminal residues 203–214 and the linker domain on motions in the human topoisomerase I-DNA complex has been investigated by comparing the molecular dynamics simulations of the system with (topo70) or without (topo58/6.3) these regions. Topo58/6.3 is found to fluctuate more than topo70, indicating that the presence of the N-terminal residues and the linker domain dampens the core and C-terminal fluctuations. The MD simulation carried out on the T718A mutant enzyme complexed with its DNA substrate indicates that the single mutation confers a different dynamical behaviour compared to the wild-type enzyme. Interestingly, no changes are observed in the proximity of the mutation site, while a different flexibility is detected in regions contacting the DNA scissile strand, such as the linker and the V-shaped α-helices. The simulation results indicate a direct communication between the mutation site and regions located relatively far away, such as the linker domain, that, with their altered flexibility, confer a reduced DNA relaxation efficiency. The structural and dynamical properties of the human topoisomerase I, have also been investigated comparing the molecular dynamics simulations of the system with and without DNA. The simulations show that a charge perturbation of the salt bridge and of the hydrogen bonds present on the lips, induces the opening of the protein “clamp” and allows to observe, for the first time, that the two principal lobes of the enzyme can separate from each other to open the “clamp”. Furthermore the simulations allows to localize a hinge around which the protein lobes rotate during the opening. The stability shown by the open conformation of the enzyme suggests that we are sampling the most probably conformation, that corresponds to the open structure of the enzyme in the absence of its substrate.
Calbucci, Vittorio. "Metodi matematici nelle scienze fisiche. Praxis: software per la simulazione del comportamento delle molecole magnetiche." Doctoral thesis, Università Politecnica delle Marche, 2012. http://hdl.handle.net/11566/242063.
Повний текст джерелаIn modern and contemporary research focused on the manufacture of smaller, faster, efficient and selective products, the production of materials with a well-defined microscopic spatial arrangements, it is of vital importance for the creation of new electronic, optical or magnetic devices. A potentially attractive way of assembly and maintain such microscopically controlled structures, is the use of molecular based materials. The research on the field of molecular magnetism, is mainly focused on molecular systems containing a finite number of coupled magnetic ions. This type of magnetic nano-molecules, generally called single magnetic molecules – SMMs, are objects placed in between of the classical and quantum physics. In fact, from a classical point of view, these structure shows phenomena such as: the slow relaxation of the magnetization and a widespread magnetic hysteresis. On te contrary, due to their dimensions, such structure can also shows quantum phenomena. The molecular magnets, indeed, are characterized by phenomena like the magnetic bistability e the most important feature of the magnetic quantum tunnelling, which is a purely quantum phenomena. These are some physical characteristics of SMMs that allow a wide range of applications of which we found their use as tools for data storage and nan-scale qbits used for the realization of quantum computer. Depending on the required applications, it is possible, today, synthetize an ad hoc molecular structure able to meet all the functional requirements. To achieve this objective, it is necessary to know and fully understand the behaviour of these molecules and therefore, are needed detailed information from the experimental methods, as well as, information obtained by theoretical models. The main topics of research: implementation of a simply simulation tool – PRAXIS - that permit the understanding of the magnetic properties of the SMMs, to verify the experimental data or to be used as experimental data predictor in order to synthetize ad hoc magnetic molecular clusters with improved properties for Nano-technological applications. Following an accurate scheme based on software engineering protocol, PRAXIS has been created with to particular aims: to verify the experimental data obtained measuring the physical properties of the SMMs, and to predict them in different situations. As last feature od PRAXIS, there is the possibility of theoretical auto-assembling of a large number of magnetic molecules, modelling them in a wide range of situations.
DIANAT, BEHNOOD. "Vetri calcogenuri per applicazioni di commutazione di memorie con particolare riguardo agli aspetti di modellazione e simulazioni." Doctoral thesis, Università degli studi di Modena e Reggio Emilia, 2021. http://hdl.handle.net/11380/1244338.
Повний текст джерелаErrani, Edoardo. ""In silico" seawater." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2019. http://amslaurea.unibo.it/18101/.
Повний текст джерелаD'AGOSTINO, TOMMASO. "Enhanced sampling methods and their application in the study of molecular permeation in gram-negative bacteria." Doctoral thesis, Università degli Studi di Cagliari, 2016. http://hdl.handle.net/11584/266673.
Повний текст джерелаGABARDI, SILVIA. "First principles simulations of phase change materials for data storage." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2015. http://hdl.handle.net/10281/76292.
Повний текст джерелаPhase change materials based on chalcogenide alloys are of great technological importance because of their use in optical data storage devices (DVDs) and electronic non-volatile memories of new concept, the Phase Change Memory cell (PCM). These applications rely on a fast (50 ns) and reversible change between the crystalline and the amorphous phases upon heating. The two phases correspond to the two states of the memory that can be discriminated thanks to a large difference in their optical and electronic properties. Although Ge2Sb2Te5 (GST) is the compound presently used as active layer in PCMs, alternative materials with a higher crystallization temperature are under scrutiny in order to increase the thermal stability of the PCM devices. In this respect, we analysed, by means of ab-initio molecular dynamics simulations, different high crystallization temperature alloys with composition In3Sb1Te2, In13Sb11Te3 and Ga4Sb6Te3, which have been experimentally proposed as substitute of GST. However, the structural properties and the microscopical reason of the high thermal stability of the amorphous phases of these compounds is still unclear. We, thus, generated models of the amorphous phase of few hundreds of atoms by quenching from the melt in few hundreds of ps aiming at finding out a relation between the structural properties of the amorphous phase and the high crystallization temperature of these alloys. The topology of our amorphous models turned out to be mostly tetrahedral which differs from the octahedral-like geometry of the crystalline phases. The presence of tetrahedral structures in the amorphous which are absent in the crystalline phase, probably hinders the crystallization process resulting in a higher crystallization temperature with respect to GST which display a mostly octahedral-like structures in both amorphous and the crystalline phase. In the second part of this work we addressed the issue of the resistance drift phenomenon, which consists of an increase of the electrical resistance of the amorphous phase with time. This effect is detrimental in PCMs since it changes the electrical characteristics of the devices. This process is believed to be due to an aging of the amorphous phase which modifies during time the defect states in the proximity of the valence and conduction band edges which control the electrical conductivity. The microscopic origin of the structural relaxations leading to the drift is still unknown. To address this problem, we generated large models (about two thousand atoms) of amorphous GeTe by quenching from the melt in 100 ps with classical molecular dynamics simulations by using a neural-network potential. Once relaxed by first principles, the models showed the presence of several in-gap states localized on chains of Ge atoms. After an annealing at 500 K, performed to accelerate the drift process, Ge chains and homopolar Ge-Ge bonds reduce in number resulting in a band gap widening and a reduction of the Urbach tails at the band edges which can account for the increase of the resistance. We thus propose that the resistance drift originates from structural relaxations leading to the removal of Ge chains.