Computational prediction of neural progenitor cell fates

Understanding how stem and progenitor cells choose between alternative cell fates is a major challenge in developmental biology. Efforts to tackle this problem have been hampered by the scarcity of markers that can be used to predict cell division outcomes. Here we present a computational method, based on algorithmic information theory, to analyze dynamic features of living cells over time. Using this method, we asked whether rat retinal progenitor cells (RPCs) display characteristic phenotypes before undergoing mitosis that could foretell their fate. We predicted whether RPCs will undergo a self-renewing or terminal division with 99% accuracy, or whether they will produce two photoreceptors or another combination of offspring with 87% accuracy. Our implementation can segment, track and generate predictions for 40 cells simultaneously on a standard computer at 5 min per frame. This method could be used to isolate cell populations with specific developmental potential, enabling previously impossible investigations.

Le progiciel PoweR : un outil de recherche reproductible pour faciliter les calculs de puissance de certains tests d'hypothèses au moyen de simulations de Monte Carlo

Notre progiciel PoweR vise à faciliter l'obtention ou la vérification des études empiriques de puissance pour les tests d'ajustement. En tant que tel, il peut être considéré comme un outil de calcul de recherche reproductible, car il devient très facile à reproduire (ou détecter les erreurs) des résultats de simulation déjà publiés dans la littérature. En utilisant notre progiciel, il devient facile de concevoir de nouvelles études de simulation. Les valeurs critiques et puissances de nombreuses statistiques de tests sous une grande variété de distributions alternatives sont obtenues très rapidement et avec précision en utilisant un C/C++ et R environnement. On peut même compter sur le progiciel snow de R pour le calcul parallèle, en utilisant un processeur multicœur. Les résultats peuvent être affichés en utilisant des tables latex ou des graphiques spécialisés, qui peuvent être incorporés directement dans vos publications. Ce document donne un aperçu des principaux objectifs et les principes de conception ainsi que les stratégies d'adaptation et d'extension.

Méthode de simulation avec les variables antithétiques

Les fichiers qui accompagnent mon document ont été réalisés avec le logiciel Latex et les simulations ont été réalisés par Splus(R).

Étude des artefacts en tomodensitométrie par simulation Monte Carlo

En radiothérapie, la tomodensitométrie (CT) fournit l’information anatomique du patient utile au calcul de dose durant la planification de traitement. Afin de considérer la composition hétérogène des tissus, des techniques de calcul telles que la méthode Monte Carlo sont nécessaires pour calculer la dose de manière exacte. L’importation des images CT dans un tel calcul exige que chaque voxel exprimé en unité Hounsfield (HU) soit converti en une valeur physique telle que la densité électronique (ED). Cette conversion est habituellement effectuée à l’aide d’une courbe d’étalonnage HU-ED. Une anomalie ou artefact qui apparaît dans une image CT avant l’étalonnage est susceptible d’assigner un mauvais tissu à un voxel. Ces erreurs peuvent causer une perte cruciale de fiabilité du calcul de dose. Ce travail vise à attribuer une valeur exacte aux voxels d’images CT afin d’assurer la fiabilité des calculs de dose durant la planification de traitement en radiothérapie. Pour y parvenir, une étude est réalisée sur les artefacts qui sont reproduits par simulation Monte Carlo. Pour réduire le temps de calcul, les simulations sont parallélisées et transposées sur un superordinateur. Une étude de sensibilité des nombres HU en présence d’artefacts est ensuite réalisée par une analyse statistique des histogrammes. À l’origine de nombreux artefacts, le durcissement de faisceau est étudié davantage. Une revue sur l’état de l’art en matière de correction du durcissement de faisceau est présentée suivi d’une démonstration explicite d’une correction empirique.

Simulation of the postoperative trunk appearance in scoliosis surgery

Persistence of external trunk asymmetry after scoliosis surgical treatment is frequent and difficult to predict by clinicians. This is a significant problem considering that correction of the apparent deformity is a major factor of satisfaction for the patients. A simulation of the correction on the external appearance would allow the clinician to illustrate to the patient the potential result of the surgery and would help in deciding on a surgical strategy that could most improve his/her appearance. We describe a method to predict the scoliotic trunk shape after a spine surgical intervention. The capability of our method was evaluated using real data of scoliotic patients. Results of the qualitative evaluation were very promising and a quantitative evaluation based on the comparison of the simulated and the actual postoperative trunk surface showed an adequate accuracy for clinical assessment. The required short simulation time also makes our approach an eligible candidate for a clinical environment demanding interactive simulations.

CFD Simulation of Multiphase Reactors

Regional Research Laboratory

Studies Using Computer Simulation Models to Solve Problems Related to Logistics Terminals

This thesis deals with the use of simulation as a problem-solving tool to solve a few logistic system related problems. More specifically it relates to studies on transport terminals. Transport terminals are key elements in the supply chains of industrial systems. One of the problems related to use of simulation is that of the multiplicity of models needed to study different problems. There is a need for development of methodologies related to conceptual modelling which will help reduce the number of models needed. Three different logistic terminal systems Viz. a railway yard, container terminal of apart and airport terminal were selected as cases for this study. The standard methodology for simulation development consisting of system study and data collection, conceptual model design, detailed model design and development, model verification and validation, experimentation, and analysis of results, reporting of finding were carried out. We found that models could be classified into tightly pre-scheduled, moderately pre-scheduled and unscheduled systems. Three types simulation models( called TYPE 1, TYPE 2 and TYPE 3) of various terminal operations were developed in the simulation package Extend. All models were of the type discrete-event simulation. Simulation models were successfully used to help solve strategic, tactical and operational problems related to three important logistic terminals as set in our objectives. From the point of contribution to conceptual modelling we have demonstrated that clubbing problems into operational, tactical and strategic and matching them with tightly pre-scheduled, moderately pre-scheduled and unscheduled systems is a good workable approach which reduces the number of models needed to study different terminal related problems.

Monte Carlo simulation of interface alloying

An Ising-like model, with interactions ranging up to next-nearest-neighbor pairs, is used to simulate the process of interface alloying. Interactions are chosen to stabilize an intermediate "antiferromagnetic" ordered structure. The dynamics proceeds exclusively by atom-vacancy exchanges. In order to characterize the process, the time evolution of the width of the intermediate ordered region and the diffusion length is studied. Both lengths are found to follow a power-law evolution with exponents depending on the characteristic features of the model.

Modeling premartensitic effects in Ni2MnGa: A mean-field and Monte Carlo simulation study

ic first-order transition line ending in a critical point. This critical point is responsible for the existence of large premartensitic fluctuations which manifest as broad peaks in the specific heat, not always associated with a true phase transition. The main conclusion is that premartensitic effects result from the interplay between the softness of the anomalous phonon driving the modulation and the magnetoelastic coupling. In particular, the premartensitic transition occurs when such coupling is strong enough to freeze the involved mode phonon. The implication of the results in relation to the available experimental data is discussed.

Measurement and simulation of anisotropy in the Infrared and Raman spectra of beta-FeSi2 single crystals

In this paper we show that the orthorhombic phase of FeSi2 (stable at room temperature) displays a sizable anisotropy in the infrared spectra, with minor effects in the Raman data too. This fact is not trivial at all, since the crystal structure corresponds to a moderate distortion of the fluorite symmetry. Our analysis is carried out on small single crystals grown by flux transport, through polarization-resolved far-infrared reflectivity and Raman measurements. Their interpretation has been obtained by means of the simulated spectra with tight-binding molecular dynamics.

Diffusive transport properties in monovalent and divalent metal-ion halide melts: A computer simulation study

Self- and cross-velocity correlation functions and related transport coefficients of molten salts are studied by molecular-dynamics simulation. Six representative systems are considered, i.e., NaCl and KCl alkali halides, CuCl and CuBr noble-metal halides, and SrCl2 and ZnCl2 divalent metal-ion halides. Computer simulation results are compared with experimental self-diffusion coefficients and electrical conductivities. Special attention is paid to dynamic cross correlations and their dependence on the Coulomb interactions as well as on the size and mass differences between anions and cations.

Modified Block Adaptive Predictive Coder For Speech Processing

This thesis investigated the potential use of Linear Predictive Coding in speech communication applications. A Modified Block Adaptive Predictive Coder is developed, which reduces the computational burden and complexity without sacrificing the speech quality, as compared to the conventional adaptive predictive coding (APC) system. For this, changes in the evaluation methods have been evolved. This method is as different from the usual APC system in that the difference between the true and the predicted value is not transmitted. This allows the replacement of the high order predictor in the transmitter section of a predictive coding system, by a simple delay unit, which makes the transmitter quite simple. Also, the block length used in the processing of the speech signal is adjusted relative to the pitch period of the signal being processed rather than choosing a constant length as hitherto done by other researchers. The efficiency of the newly proposed coder has been supported with results of computer simulation using real speech data. Three methods for voiced/unvoiced/silent/transition classification have been presented. The first one is based on energy, zerocrossing rate and the periodicity of the waveform. The second method uses normalised correlation coefficient as the main parameter, while the third method utilizes a pitch-dependent correlation factor. The third algorithm which gives the minimum error probability has been chosen in a later chapter to design the modified coder The thesis also presents a comparazive study beh-cm the autocorrelation and the covariance methods used in the evaluaiicn of the predictor parameters. It has been proved that the azztocorrelation method is superior to the covariance method with respect to the filter stabf-it)‘ and also in an SNR sense, though the increase in gain is only small. The Modified Block Adaptive Coder applies a switching from pitch precitzion to spectrum prediction when the speech segment changes from a voiced or transition region to an unvoiced region. The experiments cont;-:ted in coding, transmission and simulation, used speech samples from .\£=_‘ajr2_1a:r1 and English phrases. Proposal for a speaker reecgnifion syste: and a phoneme identification system has also been outlized towards the end of the thesis.

Numerical Simulation of Two-Part Underwater Towing System

The motion instability is an important issue that occurs during the operation of towed underwater vehicles (TUV), which considerably affects the accuracy of high precision acoustic instrumentations housed inside the same. Out of the various parameters responsible for this, the disturbances from the tow-ship are the most significant one. The present study focus on the motion dynamics of an underwater towing system with ship induced disturbances as the input. The study focus on an innovative system called two-part towing. The methodology involves numerical modeling of the tow system, which consists of modeling of the tow-cables and vehicles formulation. Previous study in this direction used a segmental approach for the modeling of the cable. Even though, the model was successful in predicting the heave response of the tow-body, instabilities were observed in the numerical solution. The present study devises a simple approach called lumped mass spring model (LMSM) for the cable formulation. In this work, the traditional LMSM has been modified in two ways. First, by implementing advanced time integration procedures and secondly, use of a modified beam model which uses only translational degrees of freedoms for solving beam equation. A number of time integration procedures, such as Euler, Houbolt, Newmark and HHT-α were implemented in the traditional LMSM and the strength and weakness of each scheme were numerically estimated. In most of the previous studies, hydrodynamic forces acting on the tow-system such as drag and lift etc. are approximated as analytical expression of velocities. This approach restricts these models to use simple cylindrical shaped towed bodies and may not be applicable modern tow systems which are diversed in shape and complexity. Hence, this particular study, hydrodynamic parameters such as drag and lift of the tow-system are estimated using CFD techniques. To achieve this, a RANS based CFD code has been developed. Further, a new convection interpolation scheme for CFD simulation, called BNCUS, which is blend of cell based and node based formulation, was proposed in the study and numerically tested. To account for the fact that simulation takes considerable time in solving fluid dynamic equations, a dedicated parallel computing setup has been developed. Two types of computational parallelisms are explored in the current study, viz; the model for shared memory processors and distributed memory processors. In the present study, shared memory model was used for structural dynamic analysis of towing system, distributed memory one was devised in solving fluid dynamic equations.

Vibrational spectroscopic studies and computational study of quinoline-2-carbaldehyde benzoyl hydrazone

FT-IR spectrum of quinoline-2-carbaldehyde benzoyl hydrazone (HQb H2O) was recorded and analyzed. The synthesis and crystal structure data are also described. The vibrational wavenumbers were examined theoretically using the Gaussian03 package of programs using HF/6-31G(d) and B3LYP/6-31G(d) levels of theory. The data obtained from vibrational wavenumber calculations are used to assign vibrational bands obtained in infrared spectroscopy of the studied molecule. The first hyperpolarizability, infrared intensities and Raman activities are reported. The calculated first hyperpolarizability is comparable with the reported values of similar derivatives and is an attractive object for future studies of non-linear optics. The geometrical parameters of the title compound obtained from XRD studies are in agreement with the calculated values. The changes in the CAN bond lengths suggest an extended p-electron delocalization over quinoline and hydrazone moieties which is responsible for the non-linearity of the molecule