Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.

A Monte Carlo simulation method for globular proteins, called extended-scaled-collective-variable (ESCV) Monte Carlo, is proposed. This method combines two Monte Carlo algorithms known as entropy-sampling and scaled-collective-variable algorithms. Entropy-sampling Monte Carlo is able to sample a large configurational space even in a disordered system that has a large number of potential barriers. In contrast, scaled-collective-variable Monte Carlo provides an efficient sampling for a system whose dynamics is highly cooperative. Because a globular protein is a disordered system whose dynamics is characterized by collective motions, a combination of these two algorithms could provide an optimal Monte Carlo simulation for a globular protein. As a test case, we have carried out an ESCV Monte Carlo simulation for a cell adhesive Arg-Gly-Asp-containing peptide, Lys-Arg-Cys-Arg-Gly-Asp-Cys-Met-Asp, and determined the conformational distribution at 300 K. The peptide contains a disulfide bridge between the two cysteine residues. This bond mimics the strong geometrical constraints that result from a protein's globular nature and give rise to highly cooperative dynamics. Computation results show that the ESCV Monte Carlo was not trapped at any local minimum and that the canonical distribution was correctly determined.

Análise comparativa dos métodos da ISO 13790 e sua adequabilidade na estimativa das necessidades de energia para aquecimento e arrefecimento e da temperatura do ar interior

Tese de mestrado integrado em Engenharia da Energia e do Ambiente, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2016

Reciprocidade periférica como estratégia para aumento de centralidade: estudo de rede de citações acadêmicas

Esta tese apresenta uma configuração em que, numa rede social regida pelo princípio da ligação preferencial, nós periféricos buscam inflacionar artificialmente seus índices de centralidade, medida pelo grau de entrada, por meio do privilégio temporário da reciprocidade de ligações com outros nós periféricos. Para construir este cenário, criou-se uma rede com as características de uma rede acadêmica de citações entre artigos, em que os nós são artigos publicados por um conjunto de periódicos, e as ligações entre eles são as citações que cada artigo faz a outros artigos existentes. Esta rede foi condensada em outra, na qual os nós são os periódicos aos quais cada artigo da primeira rede está associado, e as ligações são o total de citações que os artigos de um periódico faz aos artigos de cada outro periódico. Implementou-se um método de simulação computacional, no qual, durante alguns ciclos, foram manipulados parâmetros relacionados à quantidade total de ligações (citações) entre periódicos periféricos, de forma a induzir os efeitos desejados de reciprocidade periférica, alterando a lógica de direcionamento de citações pela atribuição de maior probabilidade para que artigos de outros periódicos periféricos recebessem ligações, afastando-se da lógica da ligação preferencial, porém sem alterar qualquer outra característica intrínseca que representasse a capacidade de um artigo ou periódico atrair novas ligações. Chamou-se esta alteração da lógica de alocação de ligações entre periódicos periféricos de Comportamento Estratégico. Observou-se que o Comportamento Estratégico é capaz de trazer benefícios de centralidade medida por grau para aqueles periódicos em que ele foi induzido, e prejuízos para os demais periódicos periféricos, porém não é suficiente para que eles saiam do quartil periférico de centralidade a que pertenciam antes da manipulação dos efeitos. Além disso, observou-se que, na ausência de elementos que alterem a capacidade intrínseca de atração de ligações de um periódico, a interrupção do Comportamento Estratégico levou aos níveis anteriores de centralidade. Também se observou que o Comportamento Estratégico acarretou em alterações de centralidade medida por autovetor estatisticamente significativas, porém não esperadas, mas que, após sua interrupção, esta retornou aos patamares anteriores à indução dos efeitos.

Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda

Bistability and switching are two important aspects of the genetic regulatory network of phage. Positive and negative feedbacks are key regulatory mechanisms in this network. By the introduction of threshold values, the developmental pathway of A phage is divided into different stages. If the protein level reaches a threshold value, positive or negative feedback will be effective and regulate the process of development. Using this regulatory mechanism, we present a quantitative model to realize bistability and switching of phage based on experimental data. This model gives descriptions of decisive mechanisms for different pathways in induction. A stochastic model is also introduced for describing statistical properties of switching in induction. A stochastic degradation rate is used to represent intrinsic noise in induction for switching the system from the lysogenic pathway to the lysis pathway. The approach in this paper represents an attempt to describe the regulatory mechanism in genetic regulatory network under the influence of intrinsic noise in the framework of continuous models. (C) 2003 Elsevier Ltd. All rights reserved.

Effects of potential models on the adsorption of ethane and ethylene on graphitized thermal carbon black. Study of two-dimensional critical temperature and isosteric heat versus loading

Adsorption of ethylene and ethane on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers is studied in detail to investigate the packing efficiency, the two-dimensional critical temperature, and the variation of the isosteric heat of adsorption with loading and temperature. Here we used a Monte Carlo simulation method with a grand canonical Monte Carlo ensemble. A number of two-center Lennard-Jones (LJ) potential models are investigated to study the impact of the choice of potential models in the description of adsorption behavior. We chose two 2C-LJ potential models in our investigation of the (i) UA-TraPPE-LJ model of Martin and Siepmann (J. Phys. Chem. B 1998,102, 25692577) for ethane and Wick et al. (J. Phys. Chem. B 2000,104, 8008-8016) for ethylene and (ii) AUA4-LJ model of Ungerer et al. (J. Chem. Phys. 2000,112, 5499-5510) for ethane and Bourasseau et al. (J. Chem. Phys. 2003, 118, 3020-3034) for ethylene. These models are used to study the adsorption of ethane and ethylene on graphitized thermal carbon black. It is found that the solid-fluid binary interaction parameter is a function of adsorbate and temperature, and the adsorption isotherms and heat of adsorption are well described by both the UA-TraPPE and AUA models, although the UA-TraPPE model performs slightly better. However, the local distributions predicted by these two models are slightly different. These two models are used to explore the two-dimensional condensation for the graphitized thermal carbon black, and these values are 110 K for ethylene and 120 K for ethane.

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

Chemical modification of polymers

Based on the knowledge of PVC degradation and stabilisation, chemical modifications were imposed on degraded PVC and raw PVC with the aim of obtaining non-migrating additives. The modifications were carried out mainly in the presence of dibutyl maleate (DBM), and the resulting polymer contained dibutyl maleic residues. Such modifications result in a polymer which contain substantive additives which resist migration under aggressive environments. Previous studies have shown that stable nitroxyl radicals function as stabilisers in polymer during processing (e.g. PP, PVC) by deactivating a large number of kinetic chains via a redox process whereby the concentrations of the nitroxyl and its reduced form, the hydroxylamine, fluctuate reciprocally and rhythmically. In order to understand the major reactions involved in such systems, a simulation method was used which resulted in a mathematical model and some rate constants, explaining the kinetic behaviour exhibited by such system. In the process of forming a suitable model, two nonlinear oscillators were proposed, which could be of interest in the study of nonlinear phenomenon because of their chaotic behaviour.

GIS linked environmental process models

In recent years there has been a great effort to combine the technologies and techniques of GIS and process models. This project examines the issues of linking a standard current generation 2½d GIS with several existing model codes. The focus for the project has been the Shropshire Groundwater Scheme, which is being developed to augment flow in the River Severn during drought periods by pumping water from the Shropshire Aquifer. Previous authors have demonstrated that under certain circumstances pumping could reduce the soil moisture available for crops. This project follows earlier work at Aston in which the effects of drawdown were delineated and quantified through the development of a software package that implemented a technique which brought together the significant spatially varying parameters. This technique is repeated here, but using a standard GIS called GRASS. The GIS proved adequate for the task and the added functionality provided by the general purpose GIS - the data capture, manipulation and visualisation facilities - were of great benefit. The bulk of the project is concerned with examining the issues of the linkage of GIS and environmental process models. To this end a groundwater model (Modflow) and a soil moisture model (SWMS2D) were linked to the GIS and a crop model was implemented within the GIS. A loose-linked approach was adopted and secondary and surrogate data were used wherever possible. The implications of which relate to; justification of a loose-linked versus a closely integrated approach; how, technically, to achieve the linkage; how to reconcile the different data models used by the GIS and the process models; control of the movement of data between models of environmental subsystems, to model the total system; the advantages and disadvantages of using a current generation GIS as a medium for linking environmental process models; generation of input data, including the use of geostatistic, stochastic simulation, remote sensing, regression equations and mapped data; issues of accuracy, uncertainty and simply providing adequate data for the complex models; how such a modelling system fits into an organisational framework.

Modeling of Cylindrical Couette Flow of Rarefied Gas Between Rotating Cylinders

Петър Господинов, Добри Данков, Владимир Русинов, Стефан Стефанов - Изследвано е цилиндрично течение на Кует за разреден газ между два въртящи се цилиндъра. Получени са профилите на налягането, скоростта и температурата по метода на прякото статистическо моделиране (DSMC) и чрез числено решаване на уравненията на Навие-Стокс за свиваем флуид. Резултатите сочат много добро съвпадение за малки числа на Кнудсен Kn = 0.02. Показано е, че при различни кинематични гранични условия, газът изостава или избързва спрямо скоростта на стената, или има поведение на твърдо еластично тяло. Получените резултати са важни при решаването на неравнинни, задачи от микрофлуидиката с отчитане на ефектите на кривината.

Validation of a multi-component digital dissolution model for irregular particles

A new mesoscale simulation model for solids dissolution based on an computationally efficient and versatile digital modelling approach (DigiDiss) is considered and validated against analytical solutions and published experimental data for simple geometries. As the digital model is specifically designed to handle irregular shapes and complex multi-component structures, use of the model is explored for single crystals (sugars) and clusters. Single crystals and the cluster were first scanned using X-ray microtomography to obtain a digital version of their structures. The digitised particles and clusters were used as a structural input to digital simulation. The same particles were then dissolved in water and the dissolution process was recorded by a video camera and analysed yielding: the overall dissolution times and images of particle size and shape during the dissolution. The results demonstrate the coherence of simulation method to reproduce experimental behaviour, based on known chemical and diffusion properties of constituent phase. The paper discusses how further sophistications to the modelling approach will need to include other important effects such as complex disintegration effects (particle ejection, uncertainties in chemical properties). The nature of the digital modelling approach is well suited to for future implementation with high speed computation using hybrid conventional (CPU) and graphical processor (GPU) systems.

Spatial and temporal patterns of true bug assemblages extracted with Berlese funnels (Data to the knowledge on the ground-living Heteroptera of Hungary, No. 2)

A rich material of Heteroptera extracted with Berlese funnels by Dr. I. Loksa between 1953–1974 in Hungary, has been examined. Altogether 157 true bug species have been identified. The ground-living heteropteran assemblages collected in different plant communities, substrata, phytogeographical provinces and seasons have been compared with multivariate methods. Because of the unequal number of samples, the objects have been standardized with stochastic simulation. There are several true bug species, which have been collected in almost all of the plant communities. However, characteristic ground-living heteropteran assemblages have been found in numerous Hungarian plant community types. Leaf litter and debris seem to have characteristic bug assemblages. Some differences have also been recognised between the bug fauna of mosses growing on different surfaces. Most of the species have been found in all of the great phytogeographical provinces of Hungary. Most high-dominance species, which have been collected, can be found at the ground-level almost throughout the year. Specimens of many other species have been collected with Berlese funnels in spring, autumn and/or winter. The diversities of the ground-living heteropteran assemblages of the examined objects have also been compared.

The construction and optimization of an ion mobility spectrometer for the analysis of explosives and drugs

Today, over 15,000 Ion Mobility Spectrometry (IMS) analyzers are employed at worldwide security checkpoints to detect explosives and illicit drugs. Current portal IMS instruments and other electronic nose technologies detect explosives and drugs by analyzing samples containing the headspace air and loose particles residing on a surface. Canines can outperform these systems at sampling and detecting the low vapor pressure explosives and drugs, such as RDX, PETN, cocaine, and MDMA, because these biological detectors target the volatile signature compounds available in the headspace rather than the non-volatile parent compounds of explosives and drugs.^ In this dissertation research volatile signature compounds available in the headspace over explosive and drug samples were detected using SPME as a headspace sampling tool coupled to an IMS analyzer. A Genetic Algorithm (GA) technique was developed to optimize the operating conditions of a commercial IMS (GE Itemizer 2), leading to the successful detection of plastic explosives (Detasheet, Semtex H, and C-4) and illicit drugs (cocaine, MDMA, and marijuana). Short sampling times (between 10 sec to 5 min) were adequate to extract and preconcentrate sufficient analytes (> 20 ng) representing the volatile signatures in the headspace of a 15 mL glass vial or a quart-sized can containing ≤ 1 g of the bulk explosive or drug.^ Furthermore, a research grade IMS with flexibility for changing operating conditions and physical configurations was designed and fabricated to accommodate future research into different analytes or physical configurations. The design and construction of the FIU-IMS were facilitated by computer modeling and simulation of ion’s behavior within an IMS. The simulation method developed uses SIMION/SDS and was evaluated with experimental data collected using a commercial IMS (PCP Phemto Chem 110). The FIU-IMS instrument has comparable performance to the GE Itemizer 2 (average resolving power of 14, resolution of 3 between two drugs and two explosives, and LODs range from 0.7 to 9 ng). ^ The results from this dissertation further advance the concept of targeting volatile components to presumptively detect the presence of concealed bulk explosives and drugs by SPME-IMS, and the new FIU-IMS provides a flexible platform for future IMS research projects.^

The Construction and Optimization on an Ion Mobility Spectrometer for the Analysis of Explosives and Drugs

Today, over 15,000 Ion Mobility Spectrometry (IMS) analyzers are employed at worldwide security checkpoints to detect explosives and illicit drugs. Current portal IMS instruments and other electronic nose technologies detect explosives and drugs by analyzing samples containing the headspace air and loose particles residing on a surface. Canines can outperform these systems at sampling and detecting the low vapor pressure explosives and drugs, such as RDX, PETN, cocaine, and MDMA, because these biological detectors target the volatile signature compounds available in the headspace rather than the non-volatile parent compounds of explosives and drugs. In this dissertation research volatile signature compounds available in the headspace over explosive and drug samples were detected using SPME as a headspace sampling tool coupled to an IMS analyzer. A Genetic Algorithm (GA) technique was developed to optimize the operating conditions of a commercial IMS (GE Itemizer 2), leading to the successful detection of plastic explosives (Detasheet, Semtex H, and C-4) and illicit drugs (cocaine, MDMA, and marijuana). Short sampling times (between 10 sec to 5 min) were adequate to extract and preconcentrate sufficient analytes (> 20 ng) representing the volatile signatures in the headspace of a 15 mL glass vial or a quart-sized can containing ≤ 1 g of the bulk explosive or drug. Furthermore, a research grade IMS with flexibility for changing operating conditions and physical configurations was designed and fabricated to accommodate future research into different analytes or physical configurations. The design and construction of the FIU-IMS were facilitated by computer modeling and simulation of ion’s behavior within an IMS. The simulation method developed uses SIMION/SDS and was evaluated with experimental data collected using a commercial IMS (PCP Phemto Chem 110). The FIU-IMS instrument has comparable performance to the GE Itemizer 2 (average resolving power of 14, resolution of 3 between two drugs and two explosives, and LODs range from 0.7 to 9 ng). The results from this dissertation further advance the concept of targeting volatile components to presumptively detect the presence of concealed bulk explosives and drugs by SPME-IMS, and the new FIU-IMS provides a flexible platform for future IMS research projects.

Least Squares Approach to Inverse Problems in Musculoskeletal Biomechanics

Inverse simulations of musculoskeletal models computes the internal forces such as muscle and joint reaction forces, which are hard to measure, using the more easily measured motion and external forces as input data. Because of the difficulties of measuring muscle forces and joint reactions, simulations are hard to validate. One way of reducing errors for the simulations is to ensure that the mathematical problem is well-posed. This paper presents a study of regularity aspects for an inverse simulation method, often called forward dynamics or dynamical optimization, that takes into account both measurement errors and muscle dynamics. The simulation method is explained in detail. Regularity is examined for a test problem around the optimum using the approximated quadratic problem. The results shows improved rank by including a regularization term in the objective that handles the mechanical over-determinancy. Using the 3-element Hill muscle model the chosen regularization term is the norm of the activation. To make the problem full-rank only the excitation bounds should be included in the constraints. However, this results in small negative values of the activation which indicates that muscles are pushing and not pulling. Despite this unrealistic behavior the error maybe small enough to be accepted for specific applications. These results is a starting point start for achieving better results of inverse musculoskeletal simulations from a numerical point of view.

The gender wage gap in the public and private sectors in Bangladesh

The gender wage gap is well studied in developed countries; however, recently it has generated much interest in developing countries. This thesis addresses three issues regarding the gender wage gap in Bangladesh. Firstly, it explores the wage determinants for formal public and private sector employees in Bangladesh and examines the gender pay gap. This is the first time different decomposition methods have been used to compare the sources of the gender wage gap as well as any potential discrimination effect in the formal sector of the Bangladeshi labour market. These decomposition methods are: the original Oaxaca (1973) and Blinder (1973) decomposition methods, the Neumark (1988), Cotton (1988), and Reimers (1983) methods, and the extended Oaxaca method including both the employment selection and the double selection correction in the wage equation. In addition to mentioned methods, to quantify the gender wage gap in monetary terms, a recently developed ‘simulated change’ approach by Olsen and Walby (2004) is also applied for the first time to the Bangladeshi data. By using the Labour Force Survey 2005-06, BBS (LFS 2005-06) data results show formal sector female employees earn about 32.1 per cent less than their male counterparts. Without considering the selection correction, a large range of human capital, demographic and labour market related variables are explained less than half of the total gender wage gap (21 to 46 per cent of the total wage gap) and the major part of the wage gap is unexplained (54 to 79 per cent of the total wage gap). This could partly be attributed to discrimination. Using the double selection correction method, the decomposition results changed where a small part of the wage gap was explained by the measured characteristics (only nine per cent of the total wage gap) and a major part is attributed to the discrimination and selection effect. The selection effect also reveals that exclusion of the double selection correction might lead to an overestimation of the gender wage gap in the formal sector of Bangladesh. In addition, results based on the Olsen and Walby (2004) simulation method show that, if the other characteristics of male and female employees were similar, ‘being female’ is sufficient, to generate significantly lower wages than males in the formal sector. If females in the workplace are treated as males, without considering any other endowment increases, females could increase their earnings by 4095.3 Taka1 per year. Results also indicate that not only endowment differences in human capital and work experience related variables were important, but discrimination appears to play a significant role in the total wage gap throughout the formal sector of the Bangladeshi labour market. Secondly, the study investigates whether public sector employees enjoyed a wage premium or not, compared to the private sector and whether the gender wage gap is greater in the public sector. In addition, the research considered whether there was an impact from the inclusion of the different selection correction terms in the wage equation. In Bangladesh, public sector employees have, on average, a 60 per cent wage premium over the private sector. Using both the original Oaxaca and the extended Oaxaca methods, where selection effect is partly captured by both explained and unexplained components, and using the public sector wage structure as the basis of the non-discriminatory wage structure, these methods revealed a considerably larger portion of explained (72 - 93 per cent of the total wage gap) and a smaller portion of unexplained part of the wage gap. However, if the selection correction is considered as another component of the decomposition outcome then the major portion of the total public and private sectors wage gap is justified (explained) by the effect of the selection correction and unexplained factors. Furthermore, a large part of the wage premium exists in favour of public sector female employees compared to males and the gender wage gap is lower in the public sector than the private sector. Finally, this study compares the gender wage gap of five different occupations. The gender wage gap is associated with labour market rigidities where one of the important factors is occupational segregation where females are disproportionately distributed in occupations resulting in lower earnings. The largest gender wage gap was found in agriculture, forestry, fisheries, production and transport labour jobs (56.4 per cent) and the lowest in the professional, technical administrative and managerial jobs (22.1 per cent). Substantial differences are found in the size of the endowment gap across occupations and larger variations occurred in the adjusted wage gap which varied from 21.4 per cent in sales and service occupations, to 100 per cent in professional and technical jobs (the highest). This too can be partly explained by discrimination. A reduction in the gender wage gap is expected not only to increase national income, but also to reduce poverty and lead to better outcomes for future generations. National policy should aim to reduce the gender wage gap and achieve gender wage equality in the formal sector; for example through a targeted program to remove the gender differences in education and to reduce the skill difference, with a better child care policy to encourage labour force retention and increased labour market experience for female employees, with anti-discriminatory policies and the enforcement of existing antidiscrimination policies, and a more equal distribution of males and females across occupations.