Sharif Digital Repository

Lattice models have been previously used to model ligand diffusion on protein surfaces. Using such models, it has been shown that the presence of pathways (or 'chreodes') of consecutive residues with certain properties can decrease the number of steps required for the arrival of a ligand at the active site. In this work, we show that, based on a genetic algorithm, ligand-diffusion pathways can evolve on a protein surface, when this surface is selected for shortening the travel length toward the active site. Biological implications of these results are discussed. © 2007 Verlag Helvetica Chimica Acta AG, Zürich  

Surgical simulation systems facilitate safe and efficient training processes of surgical trainees by providing a virtual environment in which the surgical procedure can be repeated unlimitedly in a wide variety of situations. The present study attempted to develop a real time simulation system for the grasping procedure of large internal organs during laparoscopic surgery. A mass-spring-damper model was developed to simulate the nonlinear viscoelastic large deformations of the spleen tissue while interacting with a triple-jaw grasper. A novel collision detection algorithm was designed and implemented to determine the contact points between the tissue and the grasper jaws. Force or... 

To determine the outward permeability of retina-choroid-sclera (RCS) layer for different ophthalmic drugs and to develop correlations between drug physicochemical properties and RCS permeability. A finite volume model was developed to simulate pharmacokinetics in the eye following drug administration by intravitreal injection. The RCS permeability was determined for 32 compounds by best fitting the drug concentration-time profile obtained by simulation with previously reported experimental data. Multiple linear regression was then used to develop correlations between best fit RCS permeability and drugs physicochemical properties. The RCS drug permeabilities had values that ranged over 3 ×... 

The objective of this study was to propose a new analytical model for studying response of head impacts. Head is modeled by fluidfilled ellipsoidal shell of inconstant thickness impacted by a solid elastic sphere. Modeling the head as an ellipsoid is more realistic than modeling it as a sphere, the previous model existing in the literature [3]-[8]. In this model, the effect of Hertzian contact stiffness and local shell stiffness are combined to derive explicit equations for impact duration, the peak force transmitted to head, and the head injury criterion. One of the advantages of the model presented is sensitivity to the site of impact. A comparison between the present analytical results... 

Environmental impact assessment essentially depends on diverse closely connected components and variables. For this purpose, identification of the whole components is fundamentally required. This study aims to investigate environmental impact assessment of an urban man-made lake in the western part of Tehran, based on recognition of affecting components and their reciprocal effects. Since the components are not constant during the time, thus throughout the environmental impact assessment modeling study, dynamism of the relation between the components should be considered. Regarding insufficiency and uncertainty of information, an analytical method, based on expert's opinion can be applied.... 

With the success of in vitro single-molecule force measurements obtained in recent years, the next step is to perform quantitative force measurements inside a living cell. Optical traps have proven excellent tools for manipulation, also in vivo, where they can be essentially non-invasive under correct wavelength and exposure conditions. It is a pre-requisite for in vivo quantitative force measurements that a precise and reliable force calibration of the tweezers is performed. There are well-established calibration protocols in purely viscous environments; however, as the cellular cytoplasm is viscoelastic, it would be incorrect to use a calibration procedure relying on a viscous environment.... 

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system  

Neuronal synchronization plays an important role in the various functionality of nervous system such as binding, cognition, information processing, and computation. In this paper, we investigated how random and intentional failures in the nodes of a network influence its phase synchronization properties. We considered both artificially constructed networks using models such as preferential attachment, Watts-Strogatz, and Erdo{combining double acute accent} s-Rényi as well as a number of real neuronal networks. The failure strategy was either random or intentional based on properties of the nodes such as degree, clustering coefficient, betweenness centrality, and vulnerability. Hindmarsh-Rose... 

Background: Self-organization is a fundamental feature of living organisms at all hierarchical levels from molecule to organ. It has also been documented in developing embryos. Methods. In this study, a scale-invariant power law (SIPL) method has been used to study self-organization in developing embryos. The SIPL coefficient was calculated using a centro-axial skew symmetrical matrix (CSSM) generated by entering the components of the Cartesian coordinates; for each component, one CSSM was generated. A basic square matrix (BSM) was constructed and the determinant was calculated in order to estimate the SIPL coefficient. This was applied to developing C. elegans during early stages of... 

Electroporation is defined as cell membrane permeabilization under the application of electric fields. The mechanism of hydrophilic pore formation is not yet well understood. When cells are exposed to electric fields, electrical stresses act on their surfaces. These electrical stresses play a crucial role in cell membrane structural changes, which lead to cell permeabilization. These electrical stresses depend on the dielectric properties of the cell, buffer solution, and the applied electric field characteristics. In the current study, the effect of electric field frequency on the electrical stresses distribution on the cell surface and cell deformation is numerically and experimentally... 

Using an iterative kinematics-driven nonlinear finite element model, relative efficiency of individual abdominal muscles in spinal stability in upright standing posture was investigated. Effect of load height on stability and muscle activities was also computed under different coactivity levels in abdominal muscles. The internal oblique was the most efficient muscle (compared with the external oblique and rectus abdominus) in providing stability while generating smaller spinal loads with lower fatigue rate of muscles. As the weight was held higher, stability deteriorated requiring additional flexor-extensor activities. The stabilising efficacy of abdominal muscles diminished at higher... 

Statistical and biochemical studies have revealed nonrandom patterns in codon assignments. The canonical genetic code is known to be highly efficient in minimizing the effects of mistranslational errors and point mutations, since it is known that, when an amino acid is converted to another due to error, the biochemical properties of the resulted amino acid are usually very similar to those of the original one. In this study, we have taken into consideration both relative frequencies of amino acids and relative gene copy frequencies of tRNAs in genomic sequences in order to introduce a fitness function which models the mistranslational probabilities more accurately in modern organisms. The... 

Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers,... 

The meshless element-free Galerkin method was generalized and an algorithm was developed for 3D dynamic modeling of deformable bodies in real time. The efficacy of the algorithm was investigated in a 3D linear viscoelastic model of human spleen subjected to a time-varying compressive force exerted by a surgical grasper. The model remained stable in spite of the considerably large deformations occurred. There was a good agreement between the results and those of an equivalent finite element model. The computational cost, however, was much lower, enabling the proposed algorithm to be effectively used in real-time applications  

Functional connectivity in human brain can be represented as a network using electroencephalography (EEG) signals. These networks--whose nodes can vary from tens to hundreds--are characterized by neurobiologically meaningful graph theory metrics. This study investigates the degree to which various graph metrics depend upon the network size. To this end, EEGs from 32 normal subjects were recorded and functional networks of three different sizes were extracted. A state-space based method was used to calculate cross-correlation matrices between different brain regions. These correlation matrices were used to construct binary adjacency connectomes, which were assessed with regards to a number of... 

Complex networks serve as generic models for many biological systems that have been shown to share a number of common structural properties such as power-law degree distribution and small-worldness. Real-world networks are composed of building blocks called motifs that are indeed specific subgraphs of (usually) small number of nodes. Network motifs are important in the functionality of complex networks, and the role of some motifs such as feed-forward loop in many biological networks has been heavily studied. On the other hand, many biological networks have shown some degrees of robustness in terms of their efficiency and connectedness against failures in their components. In this paper we... 

Clinical and experimental observations show individual differences in the development of addiction. Increasing evidence supports the hypothesis that dopamine receptor availability in the nucleus accumbens (NAc) predisposes drug reinforcement. Here, modeling striatal-midbrain dopaminergic circuit, we propose a reinforcement learning model for addiction based on the actor-critic model of striatum. Modeling dopamine receptors in the NAc as modulators of learning rate for appetitive-but not aversive-stimuli in the critic-but not the actor-we define vulnerability to addiction as a relatively lower learning rate for the appetitive stimuli, compared to aversive stimuli, in the critic. We... 

In this paper, the synchronization behavior of the Hindmarsh-Rose neuron model over Newman-Watts networks is investigated. The uniform synchronizing coupling strength is determined through both numerically solving the network's differential equations and the master-stability-function method. As the average degree is increased, the gap between the global synchronizing coupling strength, i.e., the one obtained through the numerical analysis, and the strength necessary for the local stability of the synchronization manifold, i.e., the one obtained through the master-stability-function approach, increases. We also find that this gap is independent of network size, at least in a class of networks... 

In the past few years, a significant body of research has been devoted to designing magnetic micron scale robotic systems for minimally invasive medicine. The motion of different microorganisms is the nature's solution for efficient propulsion of these swimmers. So far, there has been a considerable effort in designing micro swimmers based on the propulsion of bacteria while the motion of numerous other microorganisms has not been a source of inspiration for designing micro swimmers yet. Inspired by propulsion of Paramecium which is a ciliate microorganism, a novel micro swimmer is proposed in this article which is capable of cargo transport. This novel swimmer is composed of multiple...