Search results for: molecular dynamics simulations

Authors: Pragathi Gurumurthy, Christina Hagen, Patricia Ulloa, Martin A. Koch, Thorsten M. Buzug

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Obstructive sleep apnea (OSA) is a sleep disorder where the patient suffers a disturbed airflow during sleep due to partial or complete occlusion of the pharyngeal airway. Recently, numerical simulations have been used to better understand the mechanism of pharyngeal collapse. However, to gain confidence in the solutions so obtained, an experimental validation is required. Therefore, in this study an experimental validation of computational fluid dynamics (CFD) used for the study of human pharyngeal flow patterns during OSA is performed. A stationary incompressible Navier-Stokes equation solved using the finite element method was used to numerically study the flow patterns in a computed tomography-based human pharynx model. The inlet flow rate was set to 250 ml/s and such that a flat profile was maintained at the inlet. The outlet pressure was set to 0 Pa. The experimental technique used for the validation of CFD of fluid flow patterns is phase contrast-MRI (PC-MRI). Using the same computed tomography data of the human pharynx as in the simulations, a phantom for the experiment was 3 D printed. Glycerol (55.27% weight) in water was used as a test fluid at 25°C. Inflow conditions similar to the CFD study were simulated using an MRI compatible flow pump (CardioFlow-5000MR, Shelley Medical Imaging Technologies). The entire experiment was done on a 3 T MR system (Ingenia, Philips) with 108 channel body coil using an RF-spoiled, gradient echo sequence. A comparison of the axial velocity obtained in the pharynx from the numerical simulations and PC-MRI shows good agreement. The region of jet impingement and recirculation also coincide, therefore validating the numerical simulations. Hence, the experimental validation proves the reliability and correctness of the numerical simulations.

Keywords: computational fluid dynamics, experimental validation, phase contrast-MRI, obstructive sleep apnea

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Authors: Chungkuk Jin, Moo-Hyun Kim, HeonYong Kang

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A surface riding (SR) wave energy converter (WEC) is designed and its feasibility and performance are numerically simulated by the author-developed floater-mooring-magnet-electromagnetics fully-coupled dynamic analysis computer program. The biggest advantage of the SR-WEC is that the performance is equally effective even in low sea states and its structural robustness is greatly improved by simply riding along the wave surface compared to other existing WECs. By the numerical simulations and actuator testing, it is clearly demonstrated that the concept works and through the optimization process, its efficiency can be improved.

Keywords: computer simulation, electromagnetics fully-coupled dynamics, floater-mooring-magnet, optimization, performance evaluation, surface riding, WEC

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Authors: Samy Madbouly

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The relaxation behavior of biorenewable castor oil-based polyurethane-lignin thin films synthesized in homogenous waterborne dispersions was investigated as a function of concentration at different temperatures and frequencies using broadband dielectric relaxation spectroscopy (BDRS). The molecular dynamics of the glass relaxation process and the local relaxation process of the PU-LS thin films were studied over a wide range of temperatures (-70 to 30 ℃) and frequencies (5 × 10−2 to 0.5 × 107 Hz) for different lignin concentration. Four relaxation processes have been observed namely; ?-, β-, γ-relaxations and ionic conductivity for pure castor oil-based PU and castor oil-lignin-based PU thin films at different temperatures and frequencies ranges. The Vogel-Fulcher-Tammann equation was found to be well described the temperature dependence of the characteristic relaxation times of the ?-relaxation process. However, on the other hand, the molecular dynamics of both β- and γ-relaxation processes were given by the Arrhenius equation. The incorporation of lignin into the castor oil-based PU significantly increased the glass transition temperature and primitivity of the thin films. In addition, the broadness, intensity, and molecular dynamics of the only observed ?-relaxation process were found to be strongly dependent on lignin concentration.

Keywords: castor oil, lignin, polyurethane, dielectric, dispersions

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Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

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In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

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Authors: Asma Poursoroush

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Solid-supported lipid bilayers are often used as a simple model for studies of biological membranes. The presence of a solid substrate that interacts attractively with lipid head-groups is expected to affect the phase behavior of the supported bilayer. Molecular dynamics simulations of a coarse-grained model are thus performed to investigate the phase behavior of supported one-component lipid bilayer membranes. Our results show that the attraction of the lipid head groups to the substrate leads to a phase behavior that is different from that of a free standing lipid bilayer. In particular, we found that the phase behaviors of the two leaflets are decoupled in the presence of a substrate. The proximal leaflet undergoes a clear gel-to-fluid phase transition at a temperature lower than that of a free standing bilayer, and that decreases with increasing strength of the substrate-lipid attraction. The distal leaflet, however, undergoes a change from a homogeneous liquid phase at high temperatures to a heterogeneous state consisting of small liquid and gel domains, with the average size of the gel domains that increases with decreasing temperature. While the chain order parameter of the proximal leaflet clearly shows a gel-fluid phase transition, the chain order parameter of the distal leaflet does not exhibit a clear phase transition. The decoupling in the phase behavior of the two leaflets is due to a non-symmteric lipid distribution in the two leaflets resulting from the presence of the substrate.

Keywords: membrane, substrate, molecular dynamics, simulation

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Authors: Dahia Chibouti, Benoit Trouette, Eric Chenier

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With the development of micro-electro-mechanical systems (MEMS), understanding fluid flow and heat transfer at the micrometer scale is crucial. In the case where the flow characteristic length scale is narrowed to around ten times the mean free path of gas molecules, the classical fluid mechanics and energy equations are still valid in the bulk flow, but particular attention must be paid to the gas/solid interface boundary conditions. Indeed, in the vicinity of the wall, on a thickness of about the mean free path of the molecules, called the Knudsen layer, the gas molecules are no longer in local thermodynamic equilibrium. Therefore, macroscopic models based on the continuity of velocity, temperature and heat flux jump conditions must be applied at the fluid/solid interface to take this non-equilibrium into account. Although these macroscopic models are widely used, the assumptions on which they depend are not necessarily verified in realistic cases. In order to get rid of these assumptions, simulations at the molecular scale are carried out to study how molecule interaction with walls can change the fluid flow and heat transfers at the vicinity of the walls. The developed approach is based on a kind of heterogeneous multi-scale method: micro-domains overlap the continuous domain, and coupling is carried out through exchanges of information between both the molecular and the continuum approaches. In practice, molecular dynamics describes the fluid flow and heat transfers in micro-domains while the Navier-Stokes and energy equations are used at larger scales. In this framework, two kinds of micro-simulation are performed: i) in bulk, to obtain the thermo-physical properties (viscosity, conductivity, ...) as well as the equation of state of the fluid, ii) close to the walls to identify the relationships between the slip velocity and the shear stress or between the temperature jump and the normal temperature gradient. The coupling strategy relies on an implicit formulation of the quantities extracted from micro-domains. Indeed, using the results of the molecular simulations, a Bayesian regression is performed in order to build continuous laws giving both the behavior of the physical properties, the equation of state and the slip relationships, as well as their uncertainties. These latter allow to set up a learning strategy to optimize the number of micro simulations. In the present contribution, the first results regarding this coupling associated with the learning strategy are illustrated through parametric studies of convergence criteria, choice of basis functions and noise of input data. Anisothermic flows of a Lennard Jones fluid in micro-channels are finally presented.

Keywords: multi-scale, microfluidics, micro-channel, hybrid approach, coupling

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Authors: Tsu-Hsu Yen

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The interfacial gas adsorption presents a frequent challenge and opportunity for micro-/nano-fluidic operation. In this study, we investigate the wettability, gas accumulation, and nanobubble formation on various homogeneous surface conditions by using MD simulation, including a series of 3D and quasi-2D argon-water-solid systems simulation. To precisely determine the wettability on various substrates, several indicators were calculated. Among these wettability indicators, the water PMF (potential of mean force) has the most correlation tendency with interfacial water molecular orientation than depletion layer width and droplet contact angle. The results reveal that the aggregation of argon molecules on substrates not only depending on the level of hydrophobicity but also determined by the competition between gas-solid and water-solid interaction as well as water molecular structure near the surface. In addition, the surface nanobubble is always observed coexisted with the gas enrichment layer. The water structure adjacent to water-gas and water-solid interfaces also plays an important factor in gas out-flux and gas aggregation, respectively. The quasi-2D simulation shows that only a slight difference in the curved argon-water interface from the plane interface which suggests no noticeable obstructing effect on gas outflux from the gas-water interfacial water networks.

Keywords: gas aggregation, interfacial nanobubble, molecular dynamics simulation, wettability

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Authors: Pardeep Bishnoi, Mayank Srivastava, Mrityunjay Kumar Sinha

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This article represents the numerical investigation of the pressure and velocity field variation of the dynamics of pendant drop formation through a capillary tube. Numerical simulations are executed using volume of fluid (VOF) method in the computational fluid dynamics (CFD). In this problem, Non Newtonian fluid is considered as dispersed fluid whereas air is considered as a continuous fluid. Pressure contours at various time steps expose that pressure varies nearly hydrostatically at each step of the dynamics of drop formation. A result also shows the pressure variation of the liquid droplet during free fall in the computational domain. The evacuation of the fluid from the necking region is also shown by the contour of the velocity field. The role of surface tension in the Pressure contour of the dynamics of drop formation is also studied.

Keywords: pressure contour, surface tension, volume of fluid, velocity field

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Authors: Yunus Onur Yildiz, Mesut Kirca

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In this study, mechanical properties of a nanoporous metal coated with a different metallic material are studied through a new atomistic modelling technique and molecular dynamics (MD) simulations. This new atomistic modelling technique is based on the Voronoi tessellation method for the purpose of geometric representation of the ligaments. With the proposed technique, atomistic models of nanoporous metals which have randomly oriented ligaments with non-uniform mass distribution along the ligament axis can be generated by enabling researchers to control both ligament length and diameter. Furthermore, by the utilization of this technique, atomistic models of coated nanoporous materials can be numerically obtained for further mechanical or thermal characterization. In general, this study consists of two stages. At the first stage, we use algorithms developed for generating atomic coordinates of the coated nanoporous material. In this regard, coordinates of randomly distributed points are determined in a controlled way to be employed in the establishment of the Voronoi tessellation, which results in randomly oriented and intersected line segments. Then, line segment representation of the Voronoi tessellation is transformed to atomic structure by a special process. This special process includes generation of non-uniform volumetric core region in which atoms can be generated based on a specific crystal structure. As an extension, this technique can be used for coating of nanoporous structures by creating another volumetric region encapsulating the core region in which atoms for the coating material are generated. The ultimate goal of the study at this stage is to generate atomic coordinates that can be employed in the MD simulations of randomly organized coated nanoporous structures. At the second stage of the study, mechanical behavior of the coated nanoporous models is investigated by examining deformation mechanisms through MD simulations. In this way, the effect of coating on the mechanical behavior of the selected material couple is investigated.

Keywords: atomistic modelling, molecular dynamic, nanoporous metals, voronoi tessellation

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Authors: An-Shik Yang, Chiang-Ho Cheng, Jen-Hao Wu, Yu-Hsuan Juan

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Natural ventilation has played an important role for many low energy-building designs. It has been also noticed as a essential subject to persistently bring the fresh cool air from the outside into a building. This study carried out the computational fluid dynamics (CFD)-based simulations to examine the natural ventilation development of a work area in a public building. The simulated results can be useful to better understand the indoor microclimate and the interaction of wind with buildings. Besides, this CFD simulation procedure can serve as an effective analysis tool to characterize the airing performance, and thereby optimize the building ventilation for strengthening the architects, planners and other decision makers on improving the natural ventilation design of public buildings.

Keywords: CFD simulations, natural ventilation, microclimate, wind environment

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Authors: Ashish Kumar Agrahari, Amit Kumar

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Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore the atomistic level impact of PIGA mutations on the structure and dynamics of the protein. In the current work, we are mainly interested to get insights into the molecular mechanism of PIGA mutations. In the initial step, we screened the most pathogenic mutations from the pool of publicly available mutations. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and subjected to 50ns molecular dynamics simulation. Our computational study suggests that four mutations are highly vulnerable to altering the structural conformation and stability of the PIGA protein, which illustrates its association with PNH and MCAHS2 phenotype.

Keywords: homology modeling, molecular dynamics simulation, missense mutations PNH, MCAHS2, PIGA

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Authors: Wataru Nakamura, Tomoaki Hashimoto, Liang-Kuang Chen

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This paper provides a state estimation method for automatic control systems of nonlinear vehicle dynamics. A nonlinear tire model is employed to represent the realistic behavior of a vehicle. In general, all the state variables of control systems are not precisedly known, because those variables are observed through output sensors and limited parts of them might be only measurable. Hence, automatic control systems must incorporate some type of state estimation. It is needed to establish a state estimation method for nonlinear vehicle dynamics with restricted measurable state variables. For this purpose, unscented Kalman filter method is applied in this study for estimating the state variables of nonlinear vehicle dynamics. The objective of this paper is to propose a state estimation method using unscented Kalman filter for nonlinear vehicle dynamics. The effectiveness of the proposed method is verified by numerical simulations.

Keywords: state estimation, control systems, observer systems, nonlinear systems

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Authors: I-Ling Chang, Jer-An Chen

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The elastic properties and fracture of two-dimensional graphene were calculated purely from the atomic bonding (stretching and bending) based on molecular mechanics method. Considering the representative unit cell of graphene under various loading conditions, the deformations of carbon bonds and the variations of the interlayer distance could be realized numerically under the geometry constraints and minimum energy assumption. In elastic region, it was found that graphene was in-plane isotropic. Meanwhile, the in-plane deformation of the representative unit cell is not uniform along armchair direction due to the discrete and non-uniform distributions of the atoms. The fracture of graphene could be predicted using fracture criteria based on the critical bond length, over which the bond would break. It was noticed that the fracture behavior were directional dependent, which was consistent with molecular dynamics simulation results.

Keywords: energy minimization, fracture, graphene, molecular mechanics

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Authors: Aude Pérard Lecomte, Georges Fokoua, Amine Mehel, Anne Tanière

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Air quality in urban areas is deteriorated by pollution, mainly due to the constant increase of the traffic of different types of ground vehicles. In particular, particulate matter pollution with important concentrations in urban areas can cause serious health issues. Characterizing and understanding particle dynamics is therefore essential to establish recommendations to improve air quality in urban areas. To analyze the effects of turbulence on particulate pollutants dispersion, the first step is to focus on the single-phase flow structure and turbulence characteristics in the wake of a heavy truck model. To achieve this, Computational Fluid Dynamics (CFD) simulations were conducted with the aim of modeling the wake airflow of a full- and reduced-scale heavy truck. The Reynolds Average Navier-Stokes (RANS) approach with the Reynolds Stress Model (RSM)as the turbulence model closure was used. The simulations highlight the apparition of a large vortex coming from the under trailer. This vortex belongs to the recirculation region, located in the near-wake of the heavy truck. These vortical structures are expected to have a strong influence on particle dynamics that are emitted by the truck.

Keywords: CDF, heavy truck, recirculation region, reduced scale

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Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structure-process-property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: biosensor, DNA, biomarker, molecular dynamics simulation

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Authors: David Nagy

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This paper exemplifies the influence of the purpose of an aircraft on the aerodynamic properties of its airfoil. In particular, the research takes into consideration two types of aircraft, namely cargo aircraft and military high-speed aircraft and compares their airfoil characteristics using their NACA airfoils as well as computational fluid dynamics. The results show that airfoils of aircraft designed for cargo have a heavier focus on maintaining a large lift force whereas speed-oriented airplanes focus on minimizing the drag force.

Keywords: aerodynamic simulation, aircraft, airfoil, computational fluid dynamics, lift to drag ratio, NACA 64-206, NACA 65-415

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Authors: Catherine Vasnetsov, Victor Vasnetsov

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Context: Thermo-responsive polymers are materials that undergo significant changes in their physical properties in response to temperature changes. These polymers have gained significant attention in research due to their potential applications in various industries and medicine. However, the molecular mechanisms underlying their behavior are not well understood, particularly in relation to cosolvency, which is crucial for practical applications. Research Aim: This study aimed to theoretically investigate the phenomenon of cosolvency in long-chain polymers using the Flory-Huggins statistical-mechanical framework. The main objective was to understand the interactions between the polymer, solvent, and cosolvent under different conditions. Methodology: The research employed a combination of Monte Carlo computer simulations and advanced machine-learning methods. The Flory-Huggins mean field theory was used as the basis for the simulations. Spinodal graphs and ternary plots were utilized to develop an initial computer model for predicting polymer behavior. Molecular dynamic simulations were conducted to mimic real-life polymer systems. Machine learning techniques were incorporated to enhance the accuracy and reliability of the simulations. Findings: The simulations revealed that the addition of very low or very high volumes of cosolvent molecules resulted in smaller radii of gyration for the polymer, indicating poor miscibility. However, intermediate volume fractions of cosolvent led to higher radii of gyration, suggesting improved miscibility. These findings provide a possible microscopic explanation for the cosolvency phenomenon in polymer systems. Theoretical Importance: This research contributes to a better understanding of the behavior of thermo-responsive polymers and the role of cosolvency. The findings provide insights into the molecular mechanisms underlying cosolvency and offer specific predictions for future experimental investigations. The study also presents a more rigorous analysis of the Flory-Huggins free energy theory in the context of polymer systems. Data Collection and Analysis Procedures: The data for this study was collected through Monte Carlo computer simulations and molecular dynamic simulations. The interactions between the polymer, solvent, and cosolvent were analyzed using the Flory-Huggins mean field theory. Machine learning techniques were employed to enhance the accuracy of the simulations. The collected data was then analyzed to determine the impact of cosolvent volume fractions on the radii of gyration of the polymer. Question Addressed: The research addressed the question of how cosolvency affects the behavior of long-chain polymers. Specifically, the study aimed to investigate the interactions between the polymer, solvent, and cosolvent under different volume fractions and understand the resulting changes in the radii of gyration. Conclusion: In conclusion, this study utilized theoretical modeling and computer simulations to investigate the phenomenon of cosolvency in long-chain polymers. The findings suggest that moderate cosolvent volume fractions can lead to improved miscibility, as indicated by higher radii of gyration. These insights contribute to a better understanding of the molecular mechanisms underlying cosolvency in polymer systems and provide predictions for future experimental studies. The research also enhances the theoretical analysis of the Flory-Huggins free energy theory.

Keywords: molecular modelling, flory-huggins, cosolvency, stimuli-responsive polymers

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

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The DNA G-quadruplex is a four-stranded DNA structure conformed by stacked planes of four base paired guanines (G-quartet). The guanine rich DNA sequences are present in many sites of genomic DNA and can potentially lead to the formation of G-quadruplexes, especially at the 3'-terminus of the human telomeric DNA with many TTAGGG repeats. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to regulate oncogene expression making the G-quadruplex an attractive target for anticancer therapy. Clearly, the G-quadruplex structured in the telomeric DNA is of fundamental importance for rational drug design. In this context, we investigate two G-quadruplex structures, the first follows from the sequence TTAGGG(TTAGGG)3TT (HUT1), and the second from AAAGGG(TTAGGG)3AA (HUT2), both in a K+ solution. We determine the free energy surfaces of the HUT1 and HUT2 structures and investigate their conformations using replica-exchange metadynamics simulations. The carbonyl-carbonyl distances belonging to different guanines residues are selected as the main collective variables to determine the free energy surfaces. The surfaces exhibit two main local minima, compatible with experiments on the conformational transformations of HUT1 and HUT2 under substitution of the K+ ions by the Na+ ions. The conformational transitions are not observed in short MD simulations without the use of the metadynamics approach. The results of this work should be of help to understand the formation and stability of human telomeric G-quadruplex in environments including the presence of K+ and Na+ ions.

Keywords: g-quadruplex, metadynamics, molecular dynamics, replica-exchange

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Authors: Sakiru Badmos, David R. Cole, Alberto Striolo

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It is known that confinement in nm-size pores affects many structural and transport properties of water and co-existing volatile species. Of particular interest for fluids in sub-surface systems, in catalysis, and in separations are reports that confinement can enhance the solubility of gases in water. Equilibrium molecular dynamics simulations were performed for aqueous H₂S confined in slit-shaped silica pores at 313K. The effect of pore width on the H₂S solubility in water was investigated. Other properties of interest include the molecular distribution of the various fluid molecules within the pores, the hydration structure for solvated H₂S molecules, and the dynamical properties of the confined fluids. The simulation results demonstrate that confinement reduces the H₂S solubility in water and that the solubility increases with pore size. Analysis of spatial distribution functions suggests that these results are due to perturbations on the coordination of water molecules around H₂S due to confinement. Confinement is found to dampen the dynamical properties of aqueous H₂S as well. Comparing the results obtained for aqueous H₂S to those reported elsewhere for aqueous CH₄, it can be concluded that H₂S permeates hydrated slit-shaped silica nano-pores faster than CH₄. In addition to contributing to better understanding the behavior of fluids in subsurface formations, these observations could also have important implications for developing new natural gas sweetening technologies.

Keywords: confinement, interfacial properties, molecular dynamic simulation, sub-surface formations

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Authors: Weirong Wang, Shenghong Huang, Xisheng Luo, Zhenyu Li

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Material mixing process and related dynamic issues at extreme compressing conditions have gained more and more concerns in last ten years because of the engineering appealings in inertial confinement fusion (ICF) and hypervelocity aircraft developments. However, there lacks models and methods that can handle fully coupled turbulent material mixing and complex fluid evolution under conditions of high energy density regime up to now. In aspects of macro hydrodynamics, three numerical methods such as direct numerical simulation (DNS), large eddy simulation (LES) and Reynolds-averaged Navier–Stokes equations (RANS) has obtained relative acceptable consensus under the conditions of low energy density regime. However, under the conditions of high energy density regime, they can not be applied directly due to occurrence of dissociation, ionization, dramatic change of equation of state, thermodynamic properties etc., which may make the governing equations invalid in some coupled situations. However, in view of micro/meso scale regime, the methods based on Molecular Dynamics (MD) as well as Monte Carlo (MC) model are proved to be promising and effective ways to investigate such issues. In this study, both classical MD and first-principle based electron force field MD (eFF-MD) methods are applied to investigate Richtmyer-Meshkov Instability of metal Lithium and gas Hydrogen (Li-H2) interface mixing at different shock loading speed ranging from 3 km/s to 30 km/s. It is found that: 1) Classical MD method based on predefined potential functions has some limits in application to extreme conditions, since it cannot simulate the ionization process and its potential functions are not suitable to all conditions, while the eFF-MD method can correctly simulate the ionization process due to its ‘ab initio’ feature; 2) Due to computational cost, the eFF-MD results are also influenced by simulation domain dimensions, boundary conditions and relaxation time choices, etc., in computations. Series of tests have been conducted to determine the optimized parameters. 3) Ionization induced by strong shock compression has important effects on Li-H2 interface evolutions of RMI, indicating a new micromechanism of RMI under conditions of high energy density regime.

Keywords: first-principle, ionization, molecular dynamics, material mixture, Richtmyer-Meshkov instability

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Authors: Aliyu Adamu, Fahrul Huyop, Roswanira Abdul Wahab, Mohd Shahir Shamsir

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Halogenated organic compounds occur in huge amount in biosphere. This is attributable to the diverse use of halogen-based compounds in the synthesis of various industrially important products. Halogenated compound is toxic and may persist in the environment, thereby causing serious health and environmental pollution problems. L-2-haloacid dehalogenases (EC 3.8.1.2) catalyse the specific cleavage of carbon-halogen bond in L-isomers of halogenated compounds, which consequently reverse the effects of environmental halogen-associated pollution. To enhance the efficiency and utility of these enzymes, this study investigates the catalytic amino acid residues and the molecular functional mechanism of DehL, by classical molecular dynamic simulations, MM-PBSA and ab initio fragments molecular orbital (FMO) calculations. The results of the study will serve as the basis for the molecular engineering of the enzyme.

Keywords: DehL, Functional mechanism, Catalytic residues, L-2-haloacid dehalogenase

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Authors: Vagolu S. Krishna, Shan Zheng, Estharla M. Rekha, Luke W. Guddat, Dharmarajan Sriram

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Tuberculosis (TB) remains a major threat to human health. This due to the fact that current drug treatments are less than optimal as well as the rising occurrence of multi drug-resistant and extensively drug-resistant strains of the etiological agent, Mycobacterium tuberculosis (Mt). Given the wide-spread significance of this disease, we have undertaken a design and evaluation program to discover new anti-TB drug leads. Here, our attention is focused on ketol-acid reductoisomerase (KARI), the second enzyme in the branched-chain amino acid biosynthesis pathway. Importantly, this enzyme is present in bacteria but not in humans, making it an attractive proposition for drug discovery. In the present work, we used high-throughput virtual screening to identify seventeen potential inhibitors of KARI using the Birla Institute of Technology and Science in-house database. Compounds were selected based on high docking scores, which were assigned as the result of favourable interactions between the compound and the active site of KARI. The Ki values for two leads, compounds 14 and 16 are 3.71 and 3.06 µM, respectively for Mt KARI. To assess the mode of binding, 100 ns molecular dynamics simulations for these two compounds in association with Mt KARI were performed and showed that the complex was stable with an average RMSD of less than 2.5 Å for all atoms. Compound 16 showed an MIC of 2.06 ± 0.91 µM and a 1.9 fold logarithmic reduction in the growth of Mt in an infected macrophage model. The two compounds exhibited low toxicity against murine macrophage RAW 264.7 cell lines. Thus, both compounds are promising candidates for development as an anti-TB drug leads.

Keywords: ketol-acid reductoisomerase, macrophage, molecular docking and dynamics, tuberculosis

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: Anuraj Singh

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The complex dynamics is explored in a prey predator system with multiple delays. The predator dynamics is governed by Leslie-Gower scheme. The existence of periodic solutions via Hopf bifurcation with respect to delay parameters is established. To substantiate analytical findings, numerical simulations are performed. The system shows rich dynamic behavior including chaos and limit cycles.

Keywords: chaos, Hopf bifurcation, stability, time delay

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Authors: P. Haldar, P. Ghosh, S. Ghoshdastidar, K. Kargupta

Abstract:

In polymer electrolyte membrane fuel cells (PEMFC), the membrane electrode assembly (MEA) is consisting of two platinum coated carbon electrodes, sandwiched with one proton conducting phosphoric acid doped polymeric membrane. Due to low mechanical stability, flooding and fuel cell crossover, application of phosphoric acid in polymeric membrane is very critical. Phosphorous and silica based 3D inorganic gel gains the attention in the field of supercapacitors, fuel cells and metal hydrate batteries due to its thermally stable highly proton conductive behavior. Also as a large amount of water molecule and phosphoric acid can easily get trapped in Si-O-Si network cavities, it causes a prevention in the leaching out. In this study, we have performed molecular dynamics (MD) simulation and first principle calculations to understand the structural, electronics and electrochemical and morphological behavior of this inorganic gel at various P to Si ratios. We have used dipole-dipole interactions, H bonding, and van der Waals forces to study the main interactions between the molecules. A 'structure property-performance' mapping is initiated to determine optimum P to Si ratio for best proton conductivity. We have performed the MD simulations at various temperature to understand the temperature dependency on proton conductivity. The observed results will propose a model which fits well with experimental data and other literature values. We have also studied the mechanism behind proton conductivity. And finally we have proposed a structure for the gel paste with optimum P to Si ratio.

Keywords: first principle calculation, molecular dynamics simulation, phosphorous and silica based 3D inorganic gel, polymer electrolyte membrane fuel cells, proton conductivity

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Authors: Sirilak Kongkaew, Pathumwadee Yodmanee, Nopporn Kaiyawet, Arthitaya Meeprasert, Thanyada Rungrotmongkol, Toshikatsu Kaburaki, Hiroshi Noguchi, Fujio Takeuch, Nawee Kungwan, Supot Hannongbua

Abstract:

Behçet’s disease (BD) is a genetic autoimmune expressed by multisystemic inflammatory disorder mostly occurred at the skin, joints, gastrointestinal tract, and genitalia, including ocular, oral, genital, and central nervous systems. Most BD patients in Japan and Korea were strongly indicated by the genetic factor namely HLA-B*51 (especially, HLA-B*51:01) marker in HMC class I, while HLA-A*26:01 allele has been detected from the BD patients in Greek, Japan, and Taiwan. To understand the selective binding of the MICA-TM peptide towards the HLAs associated with BD, the molecular dynamics simulations were applied on the four HLA alleles (B*51:01, B*35:01, A*26:01, and A*11:01) in complex with such peptide. As a result, the key residues in the binding groove of HLA protein which play an important role in the MICA-TM peptide binding and stabilization were revealed. The Van der Waals force was found to be the main protein-protein interaction. Based on the binding free energy prediction by MM/PBSA method, the MICA-TM peptide interacted stronger to the HLA alleles associated to BD in the identical class by 7-12 kcal/mol. The obtained results from the present study could help to differentiate the HLA alleles and explain a source of Behçet’s disease.

Keywords: Behçet’s disease, MD simulations, HMC class I, autoimmune

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Authors: Francesca Risplendi, Li-Chiang Lin, Jeffrey C. Grossman, Giancarlo Cicero

Abstract:

Desalination is one of the most employed approaches to supply water in the context of a rapidly growing global water shortage. However, the most popular water filtration method available is the reverse osmosis (RO) technique, still suffers from important drawbacks, such as a large energy demands and high process costs. In addition some serious limitations have been recently discovered, among them, the boron problem seems to have a critical meaning. Boron has been found to have a dual effect on the living systems on Earth and the difference between boron deficiency and boron toxicity levels is quite small. The aim of this project is to develop a new generation of RO membranes based on porous graphene or reduced graphene oxide (rGO) able to remove salts from seawater and to reduce boron concentrations in the permeate to the level that meets the drinking or process water requirements, by means of a theoretical approach based on density functional theory and classical molecular dynamics. Computer simulations have been employed to investigate the relationship between the atomic structure of nanoporous graphene or rGO monolayer and its membrane properties in RO applications (i.e. water permeability and resilience at RO pressures). In addition, an emphasis has been given to multilayer nanoporous rGO and rGO flakes based membranes. By means of non-equilibrium MD simulations, we investigated the water transport mechanism permeating through such multilayer membrane focusing on the effect of slit widths and sheet geometries. These simulations allowed us to establish the implications of these graphene based materials as promising membrane properties for desalination plants and as boron filtration.

Keywords: boron filtration, desalination, graphene membrane, reduced graphene oxide membrane

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Authors: Asho Ali

Abstract:

Tuberculosis is a disease of grave concern which infects one-third of the global population. The high incidence of tuberculosis is further compounded by the increasing emergence of drug resistant strains including multi drug resistant (MDR). Global incidence MDR-TB is ~4%. Molecular epidemiological studies, based on the assumption that patients infected with clustered strains are epidemiologically linked, have helped understand the transmission dynamics of disease. It has also helped to investigate the basis of variation in Mycobacterium tuberculosis (MTB) strains, differences in transmission, and severity of disease or drug resistance mechanisms from across the globe. This has helped in developing strategies for the treatment and prevention of the disease including MDR.

Keywords: Mycobcaterium tuberculosis, molecular epidemiology, drug resistance, disease

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Authors: Hiroyuki Aoki

Abstract:

Polymeric materials are often used in a form of thin film such as food wrap and surface coating. In such the applications, polymer films thinner than 100 nm have been often used. The thickness of such the ultra-thin film is less than the unperturbed size of a polymer chain; therefore, the polymer chain in an ultra-thin film is strongly constrained. However, the details on the constrained dynamics of polymer molecules in ultra-thin films are still unclear. In the current study, the segmental dynamics of single polymer chain was directly investigated by fluorescence microscopy. The individual chains of poly(alkyl methacrylate) labeled by a perylenediimide dye molecule were observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was directly analyzed. The segmental motion in a thin film with a thickness of 10 nm was found to be suppressed compared to that in a bulk state. The detailed analysis of the molecular motion revealed that the diffusion rate of the in-plane rotation was similar to the thin film and the bulk; on the other hand, the out-of-plane motion was restricted in a thin film. This result indicates that the spatial restriction in an ultra-thin film thinner than the unperturbed chain dimension alters the dynamics of individual molecules in a polymer system.

Keywords: polymer materials, single molecule, molecular motion, fluorescence microscopy, super-resolution techniques

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Authors: Rauan Sakenov, Peter Bukovics, Peter Gaszler, Veronika Tokacs-Kollar, Beata Bugyi

Abstract:

FH2 (formin homology-2) domains of several proteins, collectively known as formins, including DAAM, DAAM1 and mDia1, promote G-actin nucleation and elongation. FH2 domains of these formins exist as oligomers. Chain dimerization by ring structure formation serves as a structural basis for actin polymerization function of FH2 domain. Proper single chain configuration and specific interactions between its various regions are necessary for individual chains to form a dimer functional in G-actin nucleation and elongation. FH1 and WH2 domain-containing formins were shown to behave as intrinsically disordered proteins. Thus, the aim of this research was to study structural dynamics of FH2 domain of DAAM. To investigate structural features of FH2 domain of DAAM, molecular dynamics simulation of chain A of FH2 domain of DAAM solvated in water box in 50 mM NaCl was conducted at temperatures from 293.15 to 353.15K, with VMD 1.9.2, NAMD 2.14 and Amber Tools 21 using 2z6e and 1v9d PDB structures of DAAM was obtained on I-TASSER webserver. Calcium and ATP bound G-actin 3hbt PDB structure was used as a reference protein with well-described structural dynamics of denaturation. Topology and parameter information of CHARMM 2012 additive all-atom force fields for proteins, carbohydrate derivatives, water and ions were used in NAMD 2.14 and ff19SB force field for proteins in Amber Tools 21. The systems were energy minimized for the first 1000 steps, equilibrated and produced in NPT ensemble for 1ns using stochastic Langevin dynamics and the particle mesh Ewald method. Our root-mean square deviation (RMSD) analysis of molecular dynamics of chain A of FH2 domains of DAAM revealed similar insignificant changes of total molecular average RMSD values of FH2 domain of these formins at temperatures from 293.15 to 353.15K. In contrast, total molecular average RMSD values of G-actin showed considerable increase at 328K, which corresponds to the denaturation of G-actin molecule at this temperature and its transition from native, ordered, to denatured, disordered, state which is well-described in the literature. RMSD values of lasso and tail regions of chain A of FH2 domain of DAAM exhibited higher than total molecular average RMSD at temperatures from 293.15 to 353.15K. These regions are functional in intra- and interchain interactions and contain highly conserved tryptophan residues of lasso region, highly conserved GNYMN sequence of post region and amino acids of the shell of hydrophobic pocket of the salt bridge between Arg171 and Asp321, which are important for structural stability and ordered state of FH2 domain of DAAM and its functions in FH2 domain dimerization. In conclusion, higher than total molecular average RMSD values of lasso and post regions of chain A of FH2 domain of DAAM may explain disordered state of FH2 domain of DAAM at temperatures from 293.15 to 353.15K. Finally, absence of marked transition, in terms of significant changes in average molecular RMSD values between native and denatured states of FH2 domain of DAAM at temperatures from 293.15 to 353.15K, can make it possible to attribute these formins to the group of intrinsically disordered proteins rather than to the group of intrinsically ordered proteins such as G-actin.

Keywords: FH2 domain, DAAM, formins, molecular modelling, computational biophysics

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