Dynamic Simulation Program Research Articles

Simulation of fire combustion process in valve hall of DC converter power station

To investigate the fire danger of the valve hall, a 3D numerical model of the DC converter substation's valve hall is created by using the fire dynamics simulator (FDS) program and the fire burning process of the valve hall is simulated. In particular, the procedure of simulating the fire burning in the valve hall under various fire source positions is accomplished by varying certain parameters. The smoke spreading process, ambient temperature field, and heat release rate curve under various fire source placements are compared based on the results of the simulation calculations. The findings demonstrate that under various fire source locations, the valve hall's combustion process varies as well. This study compares the time for smoke to fill the entire valve hall, the maximum temperature within the valve hall, and the maximum fire source heat release efficiency in different fire scenes. The results indicate that in fire scenes where the fire source is closer to the middle position, the time for smoke to spread throughout the valve hall is shorter, and the fire source heat release rate is higher. Conversely, in fire scenes where the fire source is closer to the edge, the maximum temperature within the valve hall is higher. The numerical simulation of the valve hall in this DC converter station assessed the hazards under different fire scenes, aiming to maximize the safety of the valve hall. It provides reliable guidance for maximizing the safety of the valve hall and facilitating firefighting and rescue efforts, thus protecting personal safety and minimizing property damage.

Real-time dynamic and structural behavior estimation of a steel lazy wave riser through finite-element-based digital twin and hull-motion sensor

A digital twin (DT) method is proposed to estimate the dynamic and structural behaviors of a Steel Lazy Wave Riser (SLWR) under environmental conditions. This method uses a 1D finite element (FE) riser model that can include various loads and boundary conditions measured from sensors. We selected a spread-moored Floating Production Storage and Offloading (FPSO) vessel to validate the proposed method, which hosts multiple Production and Injection SLWRs. Using the time-domain dynamics simulation program, we built a reference model considering the fully coupled FPSO with mooring lines and risers in various wind/wave/current conditions. The synthetic sensor data, which represents the motions and internal fluid density changes, were generated from the simulation of the reference model. Then, two riser DT models, the Top Oscillation Model (TOM) and the Two-Point Oscillation Model (TPOM), were built, considering only a single riser made of the 1D FE model. TOM employed vessel motions as boundary conditions while internal fluid density and ocean current could be inputted as external loads. TPOM incorporated an additional motion sensor attached to the riser. The motion data obtained from the reference model were first inputted into the respective riser DT models. Next, we further evaluated their performance with and without the estimated ocean currents and slugs of internal fluid. The time histories, spectra, and statistical data of displacements and stresses along the riser were systematically compared and analyzed for various test cases and environments. While the hull-motion sensor alone can provide practically acceptable results using the developed methodology, additional consideration of current load and internal fluid's density variation improves the overall riser monitoring performance. The present method can significantly reduce the number of sensors compared to traditional riser monitoring methods.

Experimental study on decoupled charge blasting-induced crack propagation with parabolic shaped charge

In this study, a new parabolic shaped charge structure is proposed to realize bidirectional blasting in coal mines. To examine the fracture characteristics of rock mass induced by shaped charge structure under explosion load, a dynamic caustic experimental system is adopted. Further, the blasting-induced damage distribution characteristics of rock mass caused by different decoupling coefficients are investigated. Using polymethyl methacrylate (PMMA) as the experimental material, a two-dimensional model is established. AUTODYN, an explicit dynamics simulation program, is used to examine the initial crack generation process under shaped charge blasting. The stress wave propagation rule and the relationship between blasting damage and decoupling coefficient are explored. The results show that the parabolic shaped charge structure can control the explosion energy distribution and reduce the surrounding rock damage. When the decoupling coefficient is 2, the main crack length is optimum. During the crack propagation process, the growth rate and stress intensity factor of the main crack of the specimen show an oscillatory downward trend. Two stress concentration points are generated on either side near the main crack, forming the initial crack. When the decoupling coefficient is less than 2, long cracks exist in both the shaped and non-shaped charged directions, and the energy gathering effect is poor. When the decoupling coefficient is greater than 2, the energy gathering effect is obvious, but the main crack length is shorter.

A Study on Power Transmission Control for Applying MR Fluid Multi-Plate Clutch to Automobile Power Distribution Device

The aim of this study is to design and manufacture a multi-plate clutch system that uses magnetorheological (MR) fluid control to allow for a variable power transmission ratio in power distribution systems. MR fluid is a smart material that enables presenting a solution to the shocks and power loss that occur due to mechanical problems in power distribution systems. As such, the longitudinal and lateral dynamic properties of 4WD (four-wheel drive) vehicles were examined and analyzed to develop an algorithm to control the front/rear power distribution according to the road surface state and driving conditions. To verify the algorithm, the CarSim vehicle dynamics simulation program was adopted to perform experiments to understand the vehicle’s dynamic performance improvements and turning stability via a HILS (Hardware in the Loop) system. In this study, an MR fluid, multi-plate clutch was used that combines a dry clutch and a wet clutch using the characteristics of the MR fluid. Such a clutch was designed to enable continuous and smooth torque transmission by utilizing the strengths of each of the dry and wet clutches. The CarSim vehicle dynamics program was used to conduct the experiments, which were conducted by linking to the manufactured MR fluid clutch experimental device. The experiments investigated the dynamic performance based on the power distribution ratio by performing longitudinal flat, inclined driving and lateral DLC (double lane change) driving. In summary, this study found that it is possible to perform power transmission by applying a current to an MR fluid and forming a magnetic field to change the flow properties of the fluid to control the torque transmission ratio that occurs in an MR fluid clutch.

Coaxial Airflow 2D Planar Simulation of Millifluidic Plant-Based Caviar Generator

Millifluidic plant-based caviar generator was investigated. Effects of parameters; continuous phase flow rate, dispersed phase flow rate, and dispersed phase aperture diameter on the equivalent diameter, degree of spherical shape, and generation rate in a coaxial airflow alginate droplet generator were examined using a computational fluid dynamics (CFD) simulation program. A 2D planar simulation together with the volume of fluid (VOF) was applied to describe the phenomenon of droplet generation. Results showed that increasing the continuous phase flow rate yielded a decrease in equivalent diameter but an increase in droplet generation rate and an increase in the degree of spherical shape. Increasing the dispersed phase flow rate yielded a decrease in the degree of spherical shape but a significant increase in the droplet generation rate as well as a slight increase in equivalent diameter. Increasing the dispersed phase aperture diameter yielded an increase in equivalent diameter but a decrease in droplet generation rate and degree of spherical shape. Overall, the device could generate from 1,400–9,000 drops per hour with around 2.3–4.0 mm in size.

Molecular dynamics simulation of 100 keV argon ion radiation effects in metals and comparison with stopping and range of ions in matter code

Simulation is essential to analyse radiation-induced effects because energetic ions have short transit times within materials (Ar ions of 1 keV and 100 keV have transit times of 0.29 picoseconds and 29 femtoseconds respectively, through a 25 nm Al film). The binary collision approximation (BCA) is extensively used in simulations to study damage caused by energetic ions due to its computational efficiency. Stopping and Range of Ions in Matter (SRIM), a widely used Monte Carlo software using BCA, provides accurate ion ranges consistent with experiments. Molecular dynamics simulations are powerful computational method, where classical equations of motion are solved to track atomic movements from radiation damage, but computational resources required are heavier for this method. In our current effort, the energy transfer from 100 keV Ar+ to metal targets is analysed as a function of target properties, including melting temperature and atomic density, using these two methodologies. A detailed investigation of 100 keV Ar+ ion impact on metal targets is done using the classical Molecular Dynamics simulation program ‘MDRange’, which uses the Recoil Interaction Analysis (RIA) approximation, where the interaction between the ion and its closest neighbours is considered via a two-body potential. The correlation of energy transferred to the metal with the target properties is examined considering the physical approximations of each technique.

Carbon footprint based on lifetime productivity for future cows selected for resilience to climate-related disturbances

Droughts, which can impact feed production, are projected to become more common under future climate conditions. In light of this, breeding cattle resilient to changes in feeding regimens is increasingly becoming an important topic. Body reserves can play a crucial role when the feed resources are limited. We simulated populations of dairy cows selected with 2 different breeding goals: one reflecting the current breeding goal and the other placing weight on minimum level of body reserves in early lactation and change in body reserves during lactation. We considered this latter as a breeding goal for resilience. We used the 2 dynamic simulation programs ADAM and AQAL to predict performance of the cows after selection. In AQAL, we modeled moderate and severe drought by decreasing feed quality and quantity offered to cows during one year. We compared cows selected with the 2 breeding goals under 3 environments: without disturbances related to climate and with moderate and severe drought. In the environments without disturbances and the moderate drought, the cows selected with the current breeding goal had higher life time lactation efficiency (energy invested in milk / energy acquired from feed) and lower carbon footprint per kg protein in milk and meat than cows selected for resilience. However, with severe drought, cows selected for resilience had higher life time lactation efficiency and lower carbon footprint per kg protein in milk and meat than those selected with the current breeding goal. This suggests that cows selected for high productive performance do not perform well under very limiting conditions, leading to increased climate impact. The importance of inclusion of body reserves as a resilience trait in dairy cattle breeding depends on the future environment in which the cows will be used.

Experiment and analysis of drop-weight damping control of MR semi-active impact resistance-based hydraulic actuator

The impact vibration caused by sudden changes in the external load of hydraulic actuators reduces the service life of hydraulic components and limits the high-precision applications of hydraulic actuators. Therefore, to improve the underdamped characteristics and impact resistance of valve-controlled cylinder systems, a semi-active impact resistance control of hydraulic actuator based on magnetorheological damper (MRD) is proposed. Firstly, based on the shear force characteristics of magnetorheological fluid, a multi-stage flow channel MRD is designed, which is connected in series with the hydraulic actuator to form a hydraulic damping actuator (HDA). Meanwhile, based on the mechanical experimental data, the parameters of MRD dynamic model are identified to ensure the accuracy of MRD output force. Secondly, a drop weight impact model is established, and a sliding mode controller which can track the command current in real time is designed, so as to realize the resistance force coupling between the MRD and the hydraulic actuator for improving the impact resistance control effect. Then the dynamic performance test and impact resistance simulation program are established to verify the excellent dynamic performance and impact resistance effect of the HDA with the sliding mode control. Finally, the drop weight impact experimental platform is built. The experimental results show that under the impact with a height of 200 mm, the dynamic offset of the HDA is only −1.25 mm, and the time to return to the original position is 0.08 s, which validate the excellent performance of the proposed scheme in improving the underdamped characteristics of the valve-controlled cylinder system and the dynamic response performance of the hydraulic actuator.

Reactive molecular dynamics simulation on the disintegration of Kapton and Upilex-S during atomic oxygen impact

Polyimides are polymeric materials that are widely used in spacecraft applications owing to their unique properties. However, exposure to a low-Earth-orbit environment containing atomic oxygen (AO) results in the disintegration of polymeric materials on the surface of spacecraft, thereby affecting the lifespan. Along with the development of theoretical research, the reactive force-field (ReaxFF) interatomic potential has become a robust computational method for exploring, developing and optimizing the material properties. This study employs the ReaxFF reactive-force-field molecular dynamics simulation (ReaxFF MD) program to investigate and compare the performance of two typical polyimide materials, Kapton and Upilex-S, under the impact of AO. Various aspects such as variations in the temperature, mass loss, decomposition products, and damage propagation depth were examined. Although these materials have similar elemental composition (C/H/O/N), they have different structures. Our results indicate that AO is initially adsorbed on the surfaces of both Kapton and Upilex-S. The continuous impact of AO leads to chemical reactions between AO and Kapton/Upilex-S. Erosion proceeds from the surface toward the interior of the materials. Similar to the findings of Experiment 2 conducted by the Materials International Space Station, our results also reveal that Upilex-S exhibits a lower mass loss and erosion yield than Kapton under the same AO conditions. This difference is primarily attributed to the distinct molecular structures of both Kapton and Upilex-S. Our study could provide valuable technical support for the extensive application of Upilex-S in spacecraft.

Optimizing Parameters for an Electrical Car Employing Vehicle Dynamics Simulation Program

At the Faculty of Engineering of the University of Debrecen we have dealt with the design and construction of electric prototype race cars for more than a decade. With a focus on more conscious design and racing we developed a vehicle dynamics simulation program, which can be used to generate the dynamics functions of the cars from their technical characteristics and data. In this publication, we deal with the optimization of the technical parameters of the above-mentioned cars for various competition tasks using our simulation program. This is a completely new field of application of the used optimization methods. This concept and idea can effectively help student teams all over the world to prepare for various domestic and international competitions. One of the applied methods is a graphic procedure, the other one is the widely used “adaptive simulated annealing” (ASA). After a brief description of the simulation program, the applied optimization methods and developed MATLAB codes for them are described. Finally, to demonstrate the effectiveness of the methods, we optimize the parameters of a prototype race car for different competition tasks and present the obtained results.

Physical Therapy May Not Be Successful for Patients With Cam-Type Femoroacetabular Impingement Syndrome and May Result in Insufficient Hip Range of Motion When Femoral Anteversion Is Less Than 16° and α-Angle Is Greater Than 65°

To identify factors associated with insufficient range of motion (ROM) improvement after the posterior pelvic tilt change in cam-type femoroacetabular impingement syndrome. Preoperative computed tomography images from 71 consecutive patients with femoroacetabular impingement syndrome treated with arthroscopic cam resection were evaluated. Using a dynamic computer simulation program, 3-dimensional models with a 10° posterior pelvic tilt from the supine functional pelvic plane (baseline) were created by computed tomography models. Patients were divided into 2 groups: those who experienced >10° (effective group) and ≤10° (ineffective group) improvements in internal rotation at 90° flexion after a 10° posterior pelvic tilt. Demographic characteristics; preoperative range of internal rotation at 90° flexion; and radiographic parameters, including Tönnis grade, lateral center-edge angle, acetabular roof obliquity angle, central acetabular anteversion, cranial acetabular anteversion, femoral anteversion, and α angle, were compared in the 2 groups. Univariate and multivariable logistic regression analyses were performed to evaluate factors associated with insufficient ROM improvement following a 10° posterior pelvic tilt. The 71 patients included 58 men and 13 women, of mean age 41.4 ± 14.6 years. Posterior pelvic tilt was effective in 13 hips and ineffective in 58. Univariate analysis showed that preoperative range of internal rotation at 90°flexion, femoral anteversion, and α angle differed significantly in the 2 groups. Multivariable analysis showed that femoral anteversion <16° (odds ratio 7.4; 95% confidence interval 1.6-35; P= .012) and α angle >65° (odds ratio 6.7; 95% confidence interval 1.2-37; P= .027) were significant factors associated with insufficient ROM improvement after posterior pelvic tilt. Physical therapy may not be successful for patients with cam-type femoroacetabular impingement syndrome and may result in insufficient hip ROM when femoral anteversion is less than 16° and α-angle is greater than 65°. Patients with a prominent cam-type deformity and lower anterior femoral anteversion are at high risk of clinical failure following improvement in pelvic mobility by conservative treatment alone and are likely to benefit from surgery for cam deformity.

Façade typology development in high-rise office building envelope

AbstractThe design of the envelope in high-rise office buildings is a task of great importance as it can impact the entire building's energy performance. The study presented in this paper is an extension of a previous work reporting on the optimization of the façade and the shading systems of an east-west facing high-rise office building. This study aims to investigate the façade geometry design factors for other potential orientations, e.g., south, south-east, and south-west directions. The IDA ICE 4.8 complex dynamic building energy simulation program was used to assess thermal and lighting simulations. The optimization results revealed the best-performing façade configurations, appropriate for each orientation examined in terms of thermal comfort, visual comfort, and energy consumption.

Torque control of a 5 KW, 220 V separately excited DC motor using microcomputer

Fast torque control is crucial for various applications, including diesel-electric locomotives, electric automobiles, and steel plants. The purpose of this paper is to utilize a microcomputer to control the torque of a separately-excited DC motor fed from a single-phase semi-controlled converter. There are numerous strategies to determine torque using direct or indirect methods. The greatest issue of direct strategy using torque meters is that the measuring device must be installed between the motor and the load. In this paper, we avoid this challenge by employing the indirect approach, specifically by monitoring several DC machine-specific quantities such as voltage, current, and speed, which are easier to determine experimentally. This technology is unquestionably helpful in real-world applications since it eliminates any mechanical impact on the installation. This paper describes the system configuration and provides an explanation of the architecture and system features. The simulation of the proposed system using TUSTSIM dynamic simulation program which is capable of simulating the control system with a digital controller in the loop is presented. An implementation of microcomputer-assisted torque control of DC separately excited motor with proportional integral (PI) controllers is presented. A typical oscillography of the driving characteristics is provided along with the experimental results.

An exa-scale high-performance molecular dynamics simulation program: MODYLAS.

A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system's performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data method, requiring a significantly lower amount of data transfer compared to conventional communications, showed significantly high performance. The coordinates and forces of 101 810 176 atoms and the multipole coefficients of the subcells could be distributed to the 32 768 nodes (1 572 864 cores) in 2.3ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and fast multipole method (FMM) calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations was only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints.

Investigating the Heat Release Rate of Large-scale Calorimeter using FDS Analysis

This study aims to identify the key design factors of a large-scale calorimeter and evaluate the accuracy of the simulation results using the Fire Dynamics Simulator (FDS) program. The design specifications of a domestic large-scale calorimeter were analyzed to determine the modeling and input conditions for the simulation. The simulation results of temperature, mass flow rate, and oxygen concentration reduction inside the duct were compared with the experimental results for heptane pool fires with diameters of 1.1 m, 1.24 m, and 1.44 m, respectively. To validate the accuracy of the simulation results, the deviations, calculated using FDS for the heat release rate as the experimental value, were found to be 19.12%, 11.86%, and 0.22% for temperature, mass flow rate, and oxygen concentration, respectively. Ultimately, the results of the heat release rate inside the duct obtained by the oxygen consumption method with FDS were found to be consistent with the experimental value, within 2.58%. However, the deviation of oxygen concentration is reduced as the deviation of mass flow rate increases for a constant heat release rate. This implies that for more accurate analysis, the heat loss and shape factors in the duct should be considered.

Molecular dynamics study of the influence of cholesterol on the rigidity of an asymmetric membrane of red blood cells.

Analysis of the mechanical properties of the plasma membrane of red blood cell (RBC) is useful for the future exploration of cell-targeted methods for treatment of Alzheimer's disease. This preliminary study aimed to observe the effects cholesterol and lipid concentration/asymmetry have on the membrane rigidity and bilayer thickness. We focused on the structure-property relationship in the plasma membranes via the analysis of bending rigidity as a function of the molar concentration of the cholesterol and lipids in the plasma membrane. The plasma membrane of RBC consists mainly of cholesterol, phosphatidylcholine (PC), sphingomyelin (SM), and proteins. Cholesterol plays a key role in the plasma membrane by maintaining its viscoelasticity and structure via modulating the fluidity and rigidity of the membrane. To analyze these properties, the coarse-grained (CG) molecular dynamics (MD) simulations were performed. The membrane building included cholesterol molar concentration ranging from 10% to 30%. To replicate the asymmetry of the cell SM and PC, the molar concentrations of lipids were varied in the range of 10%-20% and 50%-80%, respectively. The initial membrane configuration was generated using CHARMM-GUI (online graphical user interface tool). The MD simulations were performed with the Gromacs (molecular dynamic simulation program) software using all-atom and coarse-grained approaches. The aggregation of cholesterol at various molar concentrations was observed along with the fluctuation of rigidity, which could be tentatively attributed to the lipid types used in the study, the ratio of cholesterol and lipids, and the use of water as a solvent for both the inner and outer leaflet. In the future we will focus on the all-atom study of the tail interactions between cholesterol and lipids in order to identify the leading factors contributing to the bending rigidity.

Applicability of the WASP Model in an Assessment of the Impact of Anthropogenic Pollution on Water Quality—Dunajec River Case Study

This article covers the analysis of the impact of agricultural and municipal pollution on surface waters in a selected pilot section of the Dunajec River in Poland. The analysis was performed using the dynamic Water Quality Analysis Simulation Program (WASP) model. The operational use of the WASP allows the assessment of current and future changes in water quality and the planning of measures to reduce adverse impacts on surface waters. Based on the acquired and processed data, the model simulated the impact of the pollutant supply on the water quality in the selected section. The simulations were carried out in three developed scenarios. The results of the simulations of the spread of pollutants in the riverbed show that the adopted scenarios, including an increased supply of pollutants and unfavorable hydrological conditions, will not adversely affect the operation and efficiency of the water intake. Thus in the considered cases, the risk will not reach an unacceptable level. However, a serious threat may be caused by the failure of the sewage treatment plant located in the vicinity of a water intake. The conducted analyses indicate that the WASP may have significant application potential in the risk assessment for surface water intakes.

A simulation-based study to evaluate the cooling potential of nocturnal radiative cooling systems for residential buildings in Egypt

During the first years of the last decade, Egypt used to face recurrent electricity cut-offs in summer. In the past few years, the electricity tariff dramatically increased. Radiative cooling to the clear night sky is a renewable energy source that represents a relative solution. The dry desert climate promotes nocturnal radiative cooling applications. This study investigates the potential of nocturnal radiative cooling systems (RCSs) to reduce the energy consumption of the residential building sector in Egypt. The system technology proposed in this work is based on uncovered solar thermal collectors integrated into the building hydronic system. By implementing different control strategies, the same system could be used for both cooling and heating applications. The goal of this paper is to analyze the performance of RCSs in residential buildings in Egypt. The dynamic simulation program TRNSYS was used to simulate the thermal behavior of the system. The relevant issues of Egypt as a case-study are firstly overviewed. Then the paper introduces the work done to develop a building model that represents a typical residential apartment in Egypt. Typical occupancy profiles were developed to define the internal thermal gains. The adopted control strategy to optimize the system operation is presented as well. To fully understand and hence evaluate the operation of the proposed RCS, four simulation cases were considered: 1. a reference case (fully passive), 2. the stand-alone operation of the RCS, 3. ideal heating & cooling operation (fully-active), and 4. the hybrid-operation (when the active cooling system is supported by the proposed RCS). The analysis considered the main three distinct climates in Egypt, represented by the cities of Alexandria, Cairo and Asyut. The hotter and drier weather conditions resulted in a higher cooling potential and larger temperature differences. The simulated cooling power in Asyut was 28.4 W/m² for a 70 m² absorber field. For a smaller field area of 10 m², the cooling power reached 109 W/m² but with humble temperature differences. To meet the rigorous thermal comfort conditions, the proposed sensible RCS cannot fully replace conventional air-conditioning units, especially in humid areas like Alexandria. When working in a hybrid system, a 10% reduction in the active cooling energy demand could be achieved in Asyut to keep the cooling set-point at 24 °C. This percentage reduction was nearly doubled when the thermal comfort set-point was increased by two degrees (26 °C). In a sensitivity analysis, external shading devices as a passive measure as well as the implementation of the Egyptian code for buildings (ECP306/1–2005) were also investigated. The analysis of this study raised other relevant aspects to discuss, e.g. system-sizing, environmental effects, limitations and recommendations.

Molecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma

PTEN, a dual-phosphatase and scaffold protein, is one of the most commonly mutated tumour suppressor gene across various cancer types in human. The aim of this study therefore was to investigate the stability, structural and functional effects, and pathogenicity of 12 missense PTEN mutations (R15S, E18G, G36R, N49I, Y68H, I101T, C105F, D109N, V133I, C136Y, R173C and N276S) found by next generation sequencing of the PTEN gene in tissue samples obtained from glioblastoma patients. Computational tools and molecular dynamic simulation programs were used to identify the deleterious effects of these mutations. Furthermore, PTEN mRNA and protein expression levels were evaluated by qRT-PCR, Western Blot, and immunohistochemistry staining methods. Various computational tools predicted strong deleterious effects for the G36R, C105F, C136Y and N276S mutations. Molecular dynamic simulation revealed a significant decrease in protein stability for the Y68H and N276S mutations when compared with the wild type protein; whereas, C105F, D109N, V133I and R173C showed partial stability reduction. Significant residual fluctuations were observed in the R15S, N49I and C136Y mutations and radius of gyration graphs revealed the most compact structure for D109N and least for C136Y. In summary, our study is the first one to show the presence of PTEN E18G, N49I, D109N and N276S mutations in glioblastoma patients; where, D109N is neutral and N276S is a damaging and disease-associated mutation. Communicated by Ramaswamy H. Sarma

Successes and Failures of Static Aptamer-Target 3D Docking Models.

While Molecular Dynamics simulation programs are probably superior for predicting the binding and affinity of aptamers and their cognate ligands, such molecular dynamics programs require more computing power and analysis time than static docking programs that are more widely accessible to the scientific community on the internet. Static docking programs can be used to investigate the geometric fit of rigid DNA or RNA aptamer 3D structures and their ligands to aid in predicting the relative affinities and cross-reactivity of various potential ligands. Herein, the author describes when such static 3D docking analysis has worked well to produce useful predictions or confirmation of high-affinity aptamer interactions or successful aptamer beacon behavior and when it has not worked well. The analysis of why failures may occur with static 3D computer models is also discussed.