Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

THz Plasma Waves in Field-Effect-Transistors: A Monte Carlo Study

Sensing with electromagnetic waves having frequencies in the Terahertz-range is a very attractive investigative method with applications in fundamental research and industrial settings. Up to now, a lot of sources and detectors are available. However, most of these systems are bulky and have to be used in controllable environments such as laboratories. In 1993 Dyakonov and Shur suggested that plasma waves developing in field-effect-transistors can be used to emit and detect THz-radiation. Later on, it was shown that these plasma waves lead to rectification and allows for building efficient detectors. In contrast to the prediction that these plasma waves lead to new promising solid-state sources, only a few weak sources are known up to now. This work studies THz plasma waves in semiconductor devices using the Monte Carlo method in order to resolve this issue. A fast Monte Carlo solver was developed implementing a nonparabolic bandstructure representation of the used semiconductors. By investigating simplified field-effect-transistors it was found that the plasma frequency follows under equilibrium conditions the analytical predictions. However, no current oscillations were found at room temperature or with a current flowing in the channel. For more complex structures, consisting of ungated and gated regions, it was found that the plasma frequency does not follow the value predicted by the dispersion relation of the gated nor the ungated device.

Plasma polymerization of C[subscript 4]F[subscript 8] thin film on high aspect ratio silicon molds

High aspect ratio polymeric micro-patterns are ubiquitous in many fields ranging from sensors, actuators, optics, fluidics and medical. Second generation PDMS molds are replicated against first generation silicon molds created by deep reactive ion etching. In order to ensure successful demolding, the silicon molds are coated with a thin layer of C[subscript 4]F[subscript 8] plasma polymer to reduce the adhesion force. Peel force and demolding status are used to determine if delamination is successful. Response surface method is employed to provide insights on how changes in coil power, passivating time and gas flow conditions affect plasma polymerization of C[subscript 4]F[subscript 8].

Factores asociados al desarrollo de eventos adversos con transfusión de plasma fresco congelado en la Fundación Cardioinfantil-Instituto de Cardiología

Objetivo: Determinar los factores asociados con reacciones adversas transfusionales al Plasma Fresco Congelado en la FCI-IC durante los años 2008-2010. Metodología: Estudio de Casos y Controles, en relación 1:3. Pacientes mayores de 18 años transfundidos con plasma fresco congelado en la FCI-IC durante los años 2008-2010. Se definieron como casos pacientes identificados a partir del registro de eventos adversos transfusionales de la FCI que presentaron una reacción adversa transfusional a Plasma Fresco Congelado de los siguientes tipos: alérgica, febril, edema pulmonar no cardiogénico, sobrecarga volumen, CID o PTT. Los controles se definieron como personas que recibieron transfusión de plasma fresco congelado y cumpliendo los criterios de selección, no presentaron reacción adversa transfusional. Resultados: La edad de los casos fue significativamente menor (52,4 vs. 60,5 p=0,001). Para las reacciones alérgicas, el número de unidades de plasma provenientes de una unidad externa (0,7 vs. 0,0 p=0,003), de una donante de sexo femenino (2,5 vs. 1,4 p=0,11) y la paridad de dichas donantes (4,0 vs. 2,6 p=0,04), fueron en promedio mayor que para los controles. La presencia de sépsis (OR:0.01, IC95%:0,01-0,87, p=0,015) y de diabetes (OR:0.9, IC95%:0,01-0,54, p=0,003) se comportaron como factores protectores para el desarrollo de una reacción alérgica. Discusión y Conclusiones: Los resultados de este trabajo son compatibles con el hecho de que las reacciones adversas transfusionales están relacionadas con plasma provenientes de un banco de sangre externo, de donantes mujeres y de mujeres con un mayor número de gestaciones.

Eficacia del plasma rico en plaquetas en procedimientos médicos estéticos faciales . Evaluación en contorno de ojos.

Introducción: En la actualidad se están implementando nuevas técnicas, para el tratamiento de líneas de expresión facial. El Plasma Rico en Plaquetas (PRP) utiliza factores de crecimiento humano autólogos con fines médicos estéticos. El objetivo de este trabajo fue evaluar el tratamiento con plasma rico en plaquetas en el manejo del rejuvenecimiento periocular. Materiales y métodos: Estudio descriptivo retrospectivo en una cohorte de 27 pacientes entre 30 a 70 años de ambos sexos,tratados con PRP sin tratamientos médicos estéticos previos . Se compararon fotografías del sistema VISIA®, previo y posterior el PRP, para determinar los cambios del área periocular. Con análisis comparativo de medias utilizando pruebas t de student. Resultados: De 27 historias clínicas revisadas 96,3% eran mujeres, la edad promedio fue de 52.67 años. Se observaron cambios clínicos satisfactorios en el manejo del foto envejecimiento periocular con mejoría estadísticamente significativa entre el promedio inicial y el post tratamiento en arrugas, textura y porfirinas (p: 0.000). No se observaron diferencias estadísticamente significativas entre los grupos de edad (p = 0,62). Los pacientes analizados posterior al tratamiento se encuentran en mejor estado que el 63,78% de la población de su mismo sexo, edad y fototipo de piel. Los eventos adversos fueron disminuyendo en su frecuencia en cada una de las sesiones siguientes. Discusión: El PRP proporciona una mejoría global en los parámetros de envejecimiento periocular lo cual se correlaciono con los estudios previos in vitro. Conclusiones: El PRP es seguro y eficaz en contorno de ojos.

Corticosterone plasma concentrations in Carioca High- and Low-Conditioned freezing rats after a fear conditioned task

Our group in the Psychology Department at Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio) developed a rat genetic model of extreme freezing in response to contextual cues in an experimental chamber previously associated with footshock. One of the lines, Carioca High Freezing (CHF), exhibits an enhanced conditioned freezing response, whereas the other line, Carioca Low Freezing (CLF), shows the opposite response. The present study investigated corticosterone concentration between these two lines of animals and a random (RND) line of rats both under basal conditions and test condition after an emotional challenge using a contextual fear conditioning protocol. Comparisons between basal and test plasma corticosterone concentrations suggested differential basal and fear-induced differences between the two lines. The differences between basal conditions is an important and relevant aspect to be considered in behavioral experiments using or assessing stress and could help to understand variability in naïve populations.

Proyecto Plasma "Metodología de análisis entre Monopolio y Monopsonio"

muestra las opciones de negociación que tienen un Monopolio y un Monopsonio, donde los agentes se encuentran obligados a variar completamente el curso de sus estrategias.

Blackbody emission under laser excitation of silicon nanopowder produced by plasma-enhanced chemical-vapor deposition

Previous results concerning radiative emission under laser irradiation of silicon nanopowder are reinterpreted in terms of thermal emission. A model is developed that considers the particles in the powder as independent, so under vacuum the only dissipation mechanism is thermal radiation. The supralinear dependence observed between the intensity of the emitted radiation and laser power is predicted by the model, as is the exponential quenching when the gas pressure around the sample increases. The analysis allows us to determine the sample temperature. The local heating of the sample has been assessed independently by the position of the transverse optical Raman mode. Finally, it is suggested that the photoluminescence observed in porous silicon and similar materials could, in some cases, be blackbody radiation

Gas collisions and pressure quenching of the photoluminescence of silicon nanopowder grown by plasma-enhanced chemical vapor deposition

The quenching of the photoluminescence of Si nanopowder grown by plasma-enhanced chemical vapor deposition due to pressure was measured for various gases ( H2, O2, N2, He, Ne, Ar, and Kr) and at different temperatures. The characteristic pressure, P0, of the general dependence I(P)=I0exp(-P/P0) is gas and temperature dependent. However, when the number of gas collisions is taken as the variable instead of pressure, then the quenching is the same within a gas family (mono- or diatomic) and it is temperature independent. So it is concluded that the effect depends on the number of gas collisions irrespective of the nature of the gas or its temperature

Avaluació de la substitució del plasma de sang per farina de rovell d’ou com a font proteica en l’alimentació de garrins en l’etapa de desmamament.

Els subproductes de l’ou, es presenten com a una alternativa viable a l’SDPP (Spray Dried Porcine Plasma), principalment per l’elevada qualitat de la seva proteïna, alhora que representen una font important d’energia i agents antimicrobians, així com de vitamines i minerals. A més, el cost que suposa la seva inclusió en alimentació garrina és inferior al del plasma i com a element afegit, es donaria sortida a les elevades quantitats de subproductes de l’ou generades cada any, no aptes per al consum humà

Analytical methodologies based on X-Ray Fluorescence Spectrometry (XRF) and Inductively Couple Plasma Spectroscopy (ICP) for the assessment of metal dispersal around mining environments

La investigació que es presenta en aquesta tesi es centra en l'aplicació i millora de metodologies analítiques existents i el desenvolupament de nous procediments que poden ser utilitzats per a l'estudi dels efectes ambientals de la dispersió dels metalls entorn a les zones mineres abandonades. En primer lloc, es van aplicar diferents procediments d'extracció simple i seqüencial per a estudiar la mobilitat, perillositat i bio-disponibilitat dels metalls continguts en residus miners de característiques diferents. Per altra banda, per a estudiar les fonts potencials de Pb en la vegetació de les zones mineres d'estudi, una metodologia basada en la utilització de les relacions isotòpiques de Pb determinades mitjançant ICP-MS va ser avaluada. Finalment, tenint en compte l'elevat nombre de mostres analitzades per a avaluar l'impacte de les activitats mineres, es va considerar apropiat el desenvolupament de mètodes analítics d'elevada productivitat. En aquest sentit la implementació d'estratègies quantitatives així com l'aplicació de les millores instrumentals en els equips de XRF han estat avaluades per a aconseguir resultats analítics fiables en l'anàlisi de plantes. A més, alguns paràmetres de qualitat com la precisió, l'exactitud i els límits de detecció han estat curosament determinats en les diverses configuracions de espectròmetres de XRF utilitzats en el decurs d'aquest treball (EDXRF, WDXRF i EDPXRF) per a establir la capacitat de la tècnica de XRF com a tècnica alternativa a les clàssiques comunament aplicades en la determinació d'elements en mostres vegetals.

Advances in animal blood processing: development of a biopreservation system and insights on the functional properties of plasma

La sang és un subproducte amb un alt potencial de valorització que s'obté en quantitats importants en els escorxadors industrials. Actualment, la majoria de sistemes de recollida de la sang no segueixen unes mesures d'higiene estrictes, pel que esdevé un producte de baixa qualitat microbiològica. Conseqüentment, l'aprofitament de la sang és una sortida poc estimulant des del punt de vista econòmic, ja que acostuma a perdre les qualitats que permetrien l'obtenció de productes d'alt valor afegit. El capítol I del present treball s'inclou dins d'un projecte que proposa la inoculació de bacteris de l'àcid làctic (LAB) com un cultiu bioconservador de la sang, un sistema senzill i de baix cost que cerca l'estabilitat de la sang, tant microbiològica com fisicoquímica, durant el període del seu emmagatzematge. El capítol II s'emmarca dins d'un projecte que cerca la millora de l'aprofitament integral de la sang que, en el cas de la fracció plasmàtica, es centra en l'estudi de la funcionalitat dels seus principals constituents. Conèixer la contribució dels components majoritaris ha de permetre la millora de la funcionalitat dels ingredients alimentaris derivats. Els resultats presentats en aquesta tesi poden ajudar a la valorització de la sang porcina d'escorxadors industrials, mitjançant els coneixements adquirits pel que fa a la millora del seu sistema de recollida i del desenvolupament d'ingredients alimentaris amb interessants propietats funcionals.

Improvement of heat-induced gel properties of porcine plasma

L'objectiu és millorar els gels de plasma porcí induïts per calor a pH àcid utilitzant transglutaminasa microbiana (MTGasa). El tractament millora textura i CRA dels gels a pH 5,5, però les millores no són suficients per recuperar les pèrdues degut a l'acidificació. L'estructura globular de les proteïnes dificulta l'atac enzimàtic. La reactivitat de l'enzim no millora amb l'addició de cisteïna a plasma amb MTGasa. El tractament del plasma amb MTGasa sota alta pressió (HP) millora la duresa dels gels. No obstant, la CRA només millora lleugerament. La duresa es pot incrementar mantenint les solucions de plasma pressuritzat sota refrigeració, encara que no millora la CRA. Es pot concloure que les pèrdues en la textura dels gels de plasma induïts per calor a pH àcid es poden recuperar parcialment tractant amb MTGasa, especialment afegint cisteïna o sota HP. Encara que la CRA només es veu lleugerament millorada en el segon cas.