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.

Effect of disease-selective predation on prey infected by contact and external sources

We propose and analyze a simple mathematical model for susceptible prey (S)–infected prey (I)–predator (P) interaction, where the susceptible prey population (S) is infected directly from external sources as well as through contact with infected class (I) and the predator completely avoids consuming the infected prey. The model is analyzed to obtain different thresholds of the key parameters under which the system exhibits stability around the biologically feasible equilibria. Through numerical simulations we display the effects of external infection and the infection through contact on the system dynamics in the absence as well as in the presence of the predator. We compare the system dynamics when infection occurs only through contact, with that when it occurs through contact and external sources. Our analysis demonstrates that under a disease-selective predation, stability and oscillations of the system is determined by two key parameters: the external infection rate and the force of infection through contact. Due to the introduction of external infection, the predator and the prey population show limit-cycle oscillations over a range parametric values. We suggest that while predicting the dynamics of such an eco-epidemiological system, the modes of infection and the infection rates might be carefully investigated.

Conservative force fields in non-Gaussian statistics

In this Letter, we determine the kappa-distribution function for a gas in the presence of an external field of force described by a potential U(r). In the case of a dilute gas, we show that the kappa-power law distribution including the potential energy factor term can rigorously be deduced in the framework of kinetic theory with basis on the Vlasov equation. Such a result is significant as a preliminary to the discussion on the role of long range interactions in the Kaniadakis thermostatistics and the underlying kinetic theory. (C) 2008 Elsevier B.V. All rights reserved.

Effects of replica running shoes upon external forces and muscle activity during running

Twelve participants ran (9 km . h(-1)) to test two types of running shoes: replica and original shoes. Ground reaction force, plantar pressure and electromyographic activity were recorded. The shoes were tested randomly and on different days. Comparisons between the two experimental conditions were made by analysis of variance (ANOVA) test (P <= 0.05). The time to first peak, loading rate of the first peak and impulse of the first 75 ms of stance were significantly different between the shoes (P <= 0.05), revealing an increase of impact forces for the replica shoes. The peak plantar pressure values were significantly higher (P <= 0.05) when wearing replica shoes. During running, the contact area was significantly smaller (P <= 0.05) for the replica shoe. The electromyographic activity of the analysed muscles did not show changes between the two shoes in running. These findings suggest that the use of replica running shoes can increase the external load applied to the human body, but may not change the muscle activity pattern during locomotion. This new mechanical situation may increase the risk of injuries in these movements.

Corporate Venture Capital: How established firms use external resources to create new competencies

This Doctoral Dissertation is triggered by an emergent trend: firms are increasingly referring to investments in corporate venture capital (CVC) as means to create new competencies and foster the search for competitive advantage through the use of external resources. CVC is generally defined as the practice by non-financial firms of placing equity investments in entrepreneurial companies. Thus, CVC can be interpreted (i) as a key component of corporate entrepreneurship - acts of organizational creation, renewal, or innovation that occur within or outside an existing organization– and (ii) as a particular form of venture capital (VC) investment where the investor is not a traditional and financial institution, but an established corporation. My Dissertation, thus, simultaneously refers to two streams of research: corporate strategy and venture capital. In particular, I directed my attention to three topics of particular relevance for better understanding the role of CVC. In the first study, I moved from the consideration that competitive environments with rapid technological changes increasingly force established corporations to access knowledge from external sources. Firms, thus, extensively engage in external business development activities through different forms of collaboration with partners. While the underlying process common to these mechanisms is one of knowledge access, they are substantially different. The aim of the first study is to figure out how corporations choose among CVC, alliance, joint venture and acquisition. I addressed this issue adopting a multi-theoretical framework where the resource-based view and real options theory are integrated. While the first study mainly looked into the use of external resources for corporate growth, in the second work, I combined an internal and an external perspective to figure out the relationship between CVC investments (exploiting external resources) and a more traditional strategy to create competitive advantage, that is, corporate diversification (based on internal resources). Adopting an explorative lens, I investigated how these different modes to renew corporate current capabilities interact to each other. More precisely, is CVC complementary or substitute to corporate diversification? Finally, the third study focused on the more general field of VC to investigate (i) how VC firms evaluate the patent portfolios of their potential investee companies and (ii) whether the ability to evaluate technology and intellectual property varies depending on the type of investors, in particular for what concern the distinction between specialized versus generalist VCs and independent versus corporate VCs. This topic is motivated by two observations. First, it is not clear yet which determinants of patent value are primarily considered by VCs in their investment decisions. Second, VCs are not all alike in terms of technological experiences and these differences need to be taken into account.

Atomic force microscopy of biomimetic systems

This thesis was driven by the ambition to create suitable model systems that mimic complex processes in nature, like intramolecular transitions, such as unfolding and refolding of proteins, or intermolecular interactions between different cell compo-nents. Novel biophysical approaches were adopted by employing atomic force mi-croscopy (AFM) as the main measurement technique due to its broad diversity. Thus, high-resolution imaging, adhesion measurements, and single-molecule force distance experiments were performed on the verge of the instrumental capabilities. As first objective, the interaction between plasma membrane and cytoskeleton, me-diated by the linker protein ezrin, was pursued. Therefore, the adsorption process and the lateral organization of ezrin on PIP2 containing solid-supported membranes were characterized and quantified as a fundament for the establishment of a biomimetic model system. As second component of the model system, actin filaments were coated on functionalized colloidal probes attached on cantilevers, serving as sensor elements. The zealous endeavor of creating this complex biomimetic system was rewarded by successful investigation of the activation process of ezrin. As a result, it can be stated that ezrin is activated by solely binding to PIP2 without any further stimulating agents. Additional cofactors may stabilize and prolong the active conformation but are not essentially required for triggering ezrin’s transformation into an active conformation. In the second project, single-molecule force distance experiments were performed on bis-loop tetra-urea calix[4]arene-catenanes with different loading rates (increase in force per second). These macromolecules were specifically designed to investigate the rupture and rejoining mechanism of hydrogen bonds under external load. The entangled loops of capsule-like molecules locked the unbound state of intramolecular hydrogen bonds mechanically, rendering a rebinding observable on the experimental time scale. In conjunction with Molecular Dynamics simulations, a three-well potential of the bond rupture process was established and all kinetically relevant parameters of the experiments were determined by means of Monte Carlo simulations and stochastic modeling. In summary, it can be stated that atomic force microscopy is an invaluable tool to scrutinize relevant processes in nature, such as investigating activation mechanisms in proteins, as shown by analysis of the interaction between F-actin and ezrin, as well as exploring fundamental properties of single hydrogen bonds that are of paramount interest for the complete understanding of complex supramolecular structures.

Effect of external electric field on hydrogen adsorption over activated carbon separated by dielectric materials

Energy crisis and worldwide environmental problem make hydrogen a prospective energy carrier. However, storage and transportation of hydrogen in large quantities at small volume is currently not practical. Lots of materials and devices have been developed for storage hydrogen, but to today none is able to meet the DOE targets. Activated carbon has been found to be a good hydrogen adsorbent due to its high surface area. However, the weak van der Waals force between hydrogen and the adsorbent has limited the adsorption capacity. Previous studies have found that enhanced adsorption can be obtained with applied electric field. Stronger interaction between the polarized hydrogen and the charged sorbents under high voltage is considered as the reason. This study was initiated to investigate if the adsorption can be further enhanced when the activated carbon particles are separated with a dielectric coating. Dielectric TiO2 nanoparticles were first utilized. Hydrogen adsorption measurements on the TiO2-coated carbon materials, with or without an external electric field, were made. The results showed that the adsorption capacity enhancement increased with the increasing amount of TiO2 nanoparticles with an applied electric field. Since the hydrogen adsorption capacity on TiO2 particles is very low and there is no hydrogen adsorption enhancement on TiO2 particles alone when electric field is applied, the effect of dielectric coating is demonstrated. Another set of experiments investigated the behavior of hydrogen adsorption over TiO2-coated activated carbon under various electric potentials. The results revealed that the hydrogen adsorption first increased and then decreased with the increase of electric field. The improved storage was due to a stronger interaction between charged carbon surface and polarized hydrogen molecule caused by field induced polarization of TiO2 coating. When the electric field was sufficient to cause considerable ionization of hydrogen, the decrease of hydrogen adsorption occurred. The current leak detected at 3000 V was a sign of ionization of hydrogen. Experiments were also carried out to examine the hydrogen adsorption performances over activated carbon separated by other dielectric materials, MgO, ZnO and BaTiO3, respectively. For the samples partitioned with MgO and ZnO, the measurements with and without an electric field indicated negligible differences. Electric field enhanced adsorption has been observed on the activated carbon separated with BaTiO3, a material with unusually high dielectric constant. Corresponding computational calculations using Density Functional Theory have been performed on hydrogen interaction with charged TiO2 molecule as well as TiO2 molecule, coronene and TiO2-doped coronene in the presence of an electric field. The simulated results were consistent with the observations from experiments, further confirming the proposed hypotheses.

Using the Own Flexibility of a Climbing Robot as a Double Force Sensor

Force sensors are used when interaction tasks are carried out by robots in general, and by climbing robots in particular. If the mechanics and electronics systems are contained inside the own robot, the robot becomes portable without external control. Commercial force sensors cannot be used due to limited space and weight. By selecting the links material with appropriate stiffness and placing strain gauges on the structure, the own robot flexibility can be used such as force sensor. Thus, forces applied on the robot tip can be measured without additional external devices. Only gauges and small internal electronic converters are necessary. This paper illustrates the proposed algorithm to achieve these measurements. Additionally, experimental results are presented.

Novel system for bite-force sensing and monitoring based on magnetic eear field communication

Intraoral devices for bite-force sensing have several applications in odontology and maxillofacial surgery, as bite-force measurements provide additional information to help understand the characteristics of bruxism disorders and can also be of help for the evaluation of post-surgical evolution and for comparison of alternative treatments. A new system for measuring human bite forces is proposed in this work. This system has future applications for the monitoring of bruxism events and as a complement for its conventional diagnosis. Bruxism is a pathology consisting of grinding or tight clenching of the upper and lower teeth, which leads to several problems such as lesions to the teeth, headaches, orofacial pain and important disorders of the temporomandibular joint. The prototype uses a magnetic field communication scheme similar to low-frequency radio frequency identification (RFID) technology (NFC). The reader generates a low-frequency magnetic field that is used as the information carrier and powers the sensor. The system is notable because it uses an intra-mouth passive sensor and an external interrogator, which remotely records and processes information regarding a patient?s dental activity. This permits a quantitative assessment of bite-force, without requiring intra-mouth batteries, and can provide supplementary information to polysomnographic recordings, current most adequate early diagnostic method, so as to initiate corrective actions before irreversible dental wear appears. In addition to describing the system?s operational principles and the manufacture of personalized prototypes, this report will also demonstrate the feasibility of the system and results from the first in vitro and in vivo trials.

Force-mediated kinetics of single P-selectin/ligand complexes observed by atomic force microscopy

Leukocytes roll along the endothelium of postcapillary venules in response to inflammatory signals. Rolling under the hydrodynamic drag forces of blood flow is mediated by the interaction between selectins and their ligands across the leukocyte and endothelial cell surfaces. Here we present force-spectroscopy experiments on single complexes of P-selectin and P-selectin glycoprotein ligand-1 by atomic force microscopy to determine the intrinsic molecular properties of this dynamic adhesion process. By modeling intermolecular and intramolecular forces as well as the adhesion probability in atomic force microscopy experiments we gain information on rupture forces, elasticity, and kinetics of the P-selectin/P-selectin glycoprotein ligand-1 interaction. The complexes are able to withstand forces up to 165 pN and show a chain-like elasticity with a molecular spring constant of 5.3 pN nm−1 and a persistence length of 0.35 nm. The dissociation constant (off-rate) varies over three orders of magnitude from 0.02 s−1 under zero force up to 15 s−1 under external applied forces. Rupture force and lifetime of the complexes are not constant, but directly depend on the applied force per unit time, which is a product of the intrinsic molecular elasticity and the external pulling velocity. The high strength of binding combined with force-dependent rate constants and high molecular elasticity are tailored to support physiological leukocyte rolling.

Cell membrane fluctuations are regulated by medium macroviscosity: Evidence for a metabolic driving force

Extracellular fluid macroviscosity (EFM), modified by macromolecular cosolvents as occurs in body fluids, has been shown to affect cell membrane protein activities but not isolated proteins. In search for the mechanism of this phenomenon, we examined the effect of EFM on mechanical fluctuations of the cell membrane of human erythrocytes. The macroviscosity of the external medium was varied by adding to it various macromolecules [dextrans (70, 500, and 2,000 kDa), polyethylene glycol (20 kDa), and carboxymethyl-cellulose (100 kDa)], which differ in size, chemical nature, and in their capacity to increase fluid viscosity. The parameters of cell membrane fluctuations (maximal amplitude and half-width of amplitude distribution) were diminished with the elevation of solvent macroviscosity, regardless of the cosolvent used to increase EFM. Because thermally driven membrane fluctuations cannot be damped by elevation of EFM, the existence of a metabolic driving force is suggested. This is supported by the finding that in ATP-depleted red blood cells elevation of EMF did not affect cell membrane fluctuations. This study demonstrates that (i) EFM is a regulator of membrane dynamics, providing a possible mechanism by which EFM affects cell membrane activities; and (ii) cell membrane fluctuations are driven by a metabolic driving force in addition to the thermal one.

Role Expectations and State Socialization: Germany's Rediscovery of the Use of Force 1990-1995

This dissertation engages the question of why German political elites accepted the use of force during the 1990s and started to commit the country's armed forces to multilateral peacekeeping missions. Previous governments of the Federal Republic had opposed foreign deployment of the military and Germany was characterized by a unique strategic culture in which the efficacy of military force was widely regarded as negative. The rediscovery of the use of force constituted a significant reorientation of German security policy with potentially profound implications for international relations. I use social role theory to explain Germany's security policy reorientation. I argue that political elites shared a national role conception of their country as a dependable and reliable ally. Role expectations of the international security environment changed as a result of a general shift to multilateral intervention as means to address emerging security problems after the Cold War. Germany's resistance to the use of force was viewed as inappropriate conduct for a power possessing the economic and military wherewithal of the Federal Republic. Elites from allied countries exerted social pressure to have Germany contribute commensurate with capabilities. German political elites adapted role behavior in response to external expectations in an effort to preserve the national role conception of a dependable and reliable ally. Security policy reorientation to maintain Germany's national role conception was pursued by conservative elites who acted as 'role entrepreneurs'. CDU/CSU politicians initiated a process of role adaptation to include the use of force for non-defensive missions. They persuaded Social Democrats and Alliance 90/Green party politicians that the maintenance of the country's role conception necessitated a reorientation in security policy to accommodate the changes in the security environment.

Multiservice helicopter external air transport : single-point load rigging procedures.

"11 February 1991"--Vol. 2, P. i.

Constraint-force-based approach of modelling compliant mechanisms: principle and application

Numerous works have been conducted on modelling basic compliant elements such as wire beams, and closed-form analytical models of most basic compliant elements have been well developed. However, the modelling of complex compliant mechanisms is still a challenging work. This paper proposes a constraint-force-based (CFB) modelling approach to model compliant mechanisms with a particular emphasis on modelling complex compliant mechanisms. The proposed CFB modelling approach can be regarded as an improved free-body- diagram (FBD) based modelling approach, and can be extended to a development of the screw-theory-based design approach. A compliant mechanism can be decomposed into rigid stages and compliant modules. A compliant module can offer elastic forces due to its deformation. Such elastic forces are regarded as variable constraint forces in the CFB modelling approach. Additionally, the CFB modelling approach defines external forces applied on a compliant mechanism as constant constraint forces. If a compliant mechanism is at static equilibrium, all the rigid stages are also at static equilibrium under the influence of the variable and constant constraint forces. Therefore, the constraint force equilibrium equations for all the rigid stages can be obtained, and the analytical model of the compliant mechanism can be derived based on the constraint force equilibrium equations. The CFB modelling approach can model a compliant mechanism linearly and nonlinearly, can obtain displacements of any points of the rigid stages, and allows external forces to be exerted on any positions of the rigid stages. Compared with the FBD based modelling approach, the CFB modelling approach does not need to identify the possible deformed configuration of a complex compliant mechanism to obtain the geometric compatibility conditions and the force equilibrium equations. Additionally, the mathematical expressions in the CFB approach have an easily understood physical meaning. Using the CFB modelling approach, the variable constraint forces of three compliant modules, a wire beam, a four-beam compliant module and an eight-beam compliant module, have been derived in this paper. Based on these variable constraint forces, the linear and non-linear models of a decoupled XYZ compliant parallel mechanism are derived, and verified by FEA simulations and experimental tests.

‘State failure’ and the extraterritorial use of force in self-defence against non-state actors

The thesis is first and foremost the examination of the notion and consequences of ‘state failure’ in international law. The disputes surrounding criteria for creation and recognition of states pertain to efforts to analyse legal and factual issues unravelling throughout the continuing existence of states, as best evidenced by the ‘state failure’ phenomenon. It is argued that although the ‘statehood’ of failed states remains uncontested, their sovereignty is increasingly considered to be dependent on the existence of effective governments. The second part of this thesis focuses on the examinations of the legal consequences of the continuing existence of failed states in the context of jus ad bellum. Since the creation of the United Nations the ability of states to resort to armed force without violating what might be considered as the single most important norm of international law, has been considerably limited. State failure and increasing importance of non-state actors has become a greatly topical issue within recent years in both scholarship and the popular imagination. There have been important legal developments within international law, which have provoked much academic, and in particular, legal commentary. On one level, the thesis contributes to this commentary. Despite the fact that the international community continues to perpetuate a notion of ‘statehood’ which allows the state-centric system of international law to exist, when dealing with practical and political realities of state failure, international law may no longer consider external sovereignty of states as an undeniable entitlement to statehood. Accordingly, the main research question of this thesis is whether the implicit and explicit invocation of the state failure provides sufficient legal basis for the intervention in self-defence against non-state actors in located in failed states. It has been argued that state failure has a profound impact, the extent of which is yet to be fully explored, on the modern landscape of peace and security.