Sumith Yesudasan | University of New Haven (original) (raw)
Papers by Sumith Yesudasan
Microsystem Technologies-micro-and Nanosystems-information Storage and Processing Systems, Jul 4, 2020
This article details the analysis of the thermo-hydraulic performance of a single-phase MEMS Heat... more This article details the analysis of the thermo-hydraulic performance of a single-phase MEMS Heat sink with pin fins integrated in micro channels. Circular pin-fins with in-line arrangement are considered in this study. The influence of operating and geometric parameters on the performance, (thermal resistance and pressure drop) are studied; the parameters considered include microchannel hydraulic diameter, microchannel spacing, substrate material, pin-fin pitch, and Reynolds number. Additionally, the performance is quantified in terms of a Figure of Merit (FOM) which is the product of normalized thermal resistance and normalized pressure drop. The thermal resistance of heat sink with pin-fin integrated in micro channels is lower than that in heat sinks without pin-fins irrespective of the Reynolds number. On the other hand, the pressure drop associated with heat sink with pin-fins integrated in microchannel is higher than that in heat sinks without pin-fins for all Reynolds number. Also, increase in hydraulic diameter leads to reduction in thermal resistance and increase in pressure drop for a specific Reynolds number. On the other hand, reduction in microchannel spacing leads to reduction in thermal resistance for a specific Reynolds number; the pressure drop is independent of the microchannel spacing. With regards to the influence of substrate material, the thermal resistance decreased with increase in thermal conductivity; the pressure drop is not influenced by changes in substrate material.
Journal of Molecular Modeling, 2018
Studies suggest that patients with deep vein thrombosis and diabetes often have hypercoagulable b... more Studies suggest that patients with deep vein thrombosis and diabetes often have hypercoagulable blood plasma, leading to a higher risk of thromboembolism formation through the rupture of blood clots, which may lead to stroke and death. Despite many advances in the field of blood clot formation and thrombosis, the influence of mechanical properties of fibrin in the formation of thromboembolisms in platelet-poor plasma is poorly understood. In this paper, we combine the concepts of reactive molecular dynamics and coarse-grained molecular modeling to predict the complex network formation of fibrin clots and the branching of fibrin monomers. The 340-kDa fibrinogen molecule was converted into a coarse-grained molecule with nine beads, and using our customized reactive potentials, we simulated the formation and polymerization process of a fibrin clot. The results show that higher concentrations of thrombin result in higher branch-point formation in the fibrin clot structure. Our results a...
Supplementary_Information_-_CATH for Glucose Concentration Affects Fibrin Clot Structure and Morp... more Supplementary_Information_-_CATH for Glucose Concentration Affects Fibrin Clot Structure and Morphology as Evidenced by Fluorescence Imaging and Molecular Simulations by Jacob E. Hood, Sumith Yesudasan, and Rodney D. Averett in Clinical and Applied Thrombosis/Hemostasis
ArXiv, 2021
Weak passwords and availability of supercomputers to password crackers make the financial institu... more Weak passwords and availability of supercomputers to password crackers make the financial institutions and businesses at stake. This calls for use of strong passwords and multi factor authentication for secure transactions. Remembering a long and complex password by humans is a daunting task and mnemonic has helped to mitigate this situation to an extent. This paper discusses creating and using long random password and storing them securely using a hybrid strategy of hash-encryption method. The hash function uses a mnemonic password based on the hotel names and other characteristics like room number, floor number and breakfast meal preferences to generate the encryption key. The random strong password can be then encrypted using the key and stored safely. A computer program named Hector is developed which demonstrates these steps and can be used to generate and store the passwords.
In this work, we investigate the pressure and density characteristics of water film when simulate... more In this work, we investigate the pressure and density characteristics of water film when simulated using the emerging technique called many body dissipative particle dynamics method. This work also layout the methodology of estimating local pressure from LAMMPS simulation using Harasima scheme. Using the triangular shaped cloud interpolation function, pressure and density are estimated at local bins and compared with the experimental database. Our results show good agreement for the molecular dynamics results of the argon system, while the many body dissipative particle model fails to simulate the water properties at room temperature. In its current form, the many body dissipative particle method cannot be used for accurate liquid vapor interfacial simulations and heat transfer studies.
Blood clots occur in the human body when they are required to prevent bleeding. In pathological s... more Blood clots occur in the human body when they are required to prevent bleeding. In pathological states such as diabetes and sickle cell disease, blood clots can also form undesirably due to hypercoagulable plasma conditions. With the continued effort in developing fibrin therapies for potential life-saving solutions, more mechanical modeling is needed to understand the properties of fibrin structures with inclusions. In this study, a fibrin matrix embedded with magnetic micro particles (MMPs) was subjected to a magnetic field to determine the magnitude of the required force to create plastic deformation within the fibrin clot. Using finite element (FE) analysis, we estimated the magnetic force from an electromagnet at a sample space located approximately 3 cm away from the coil center. This electromagnetic force coupled with gravity was applied on a fibrin mechanical system with MMPs to calculate the stresses and displacements. Using appropriate coil parameters, it was determined that application of a magnetic field of 730 A/m on the fibrin surface was necessary to achieve an electromagnetic force of 36 nN (to engender plastic deformation).
arXiv: Biological Physics, 2018
The multiscale behavior of the individual fibrin fibers and fibrin clots is modeled by coupling a... more The multiscale behavior of the individual fibrin fibers and fibrin clots is modeled by coupling atomistic simulation data and microscopic experimental data. We propose a protofibril element made up of nonlinear spring network, constructed based on the molecular simulation and atomic force microscopy results to simulate the force extension behavior of fibrin fibers. This new network model also accounts for the complex interaction of protofibrils with each other, effect of presence of solvent, Coulombic attraction and other binding forces. The network model is applied to simulate the force extension behavior of single fibrin fiber from atomic force microscopy experiments and shows good agreement. Thus validated fibrin fiber network model is then combined with a modified version of Arruda-Boyce eight chain model to estimate the force extension behavior of continuum level fibrin clot, which shows very good correlation. The results show that this network model is able to predict the beha...
In this paper, we introduce a simple yet powerful and working version of the molecular dynamics c... more In this paper, we introduce a simple yet powerful and working version of the molecular dynamics code using the Python 3.9 language. The code contents are published in the link given in the appendix 1. The structure and components of the program is given in detail using flowcharts and code snippets. The program consists of major features like velocity verlet integrator, thermostats, COM removal, input and output modules, virial, pressure, and other thermodynamic quantities estimation etc. The author believes that this program will be helpful to graduate students who perform research in molecular dynamics simulations who intend to write their own code instead of the sophisticated open source packages.
This paper investigates the improvement in solar energy collection and conversion using Al2O3-Wat... more This paper investigates the improvement in solar energy collection and conversion using Al2O3-Water nanofluids in a solar flat plate collector (SFPC). The efficiency of a solar flat plate collector using water as the fluid medium is analyzed experimentally and theoretically. For theoretical analysis, a mathematical model in MATLAB is used to simulate and is validated by the experimental results. To enhance the solar energy collection and conversion efficiency of the SFPC, Al2O3-Water nanofluid was selected as the fluid medium. The nanofluid properties like density, specific heat capacity, thermal conductivity and viscosity are analyzed and compared for several models of Al2O3-Water nanofluids and the best model was selected to modify the simulation. Effect of particle diameter in the nanofluid was found to be marginal on the nanofluid properties. The optimum volume concentration of the nanofluid was found to be 4% giving an efficiency increase of 7.78% in the SFPC over the use of wa...
Journal of Molecular Graphics and Modelling, 2018
Coupling of statistical properties from atomistic simulations to continuum is essential to model ... more Coupling of statistical properties from atomistic simulations to continuum is essential to model many multi-scale phenomena. Often, the system under consideration will be homogeneous in twodimensions (2-D). But due to the existing coupling methods, the property estimation takes place in three-dimensions (3-D) and then averaged to 2-D, which is computationally expensive due to the 3-D convolutions. A direct 2-D pressure or stress estimation model is lacking in literature. In this work, we develop a direct 2-D pressure field estimation method which is much faster than 3-D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor. This formulation will enable the study of 2-D fundamental phenomena like passive liquid flows in microlayer, as well as facilitate the coupling of atomistic and continuum simulations with reduced computational cost.
ASME 2015 13th International Conference on Nanochannels, Microchannels, and Minichannels, 2015
It is important to study contact angle of a liquid on a solid surface to understand its wetting p... more It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating the time evolution of contact angle. This is a tedious effort to do manually or with image processing algorithms. In this work we propose a new algorithm to estimate contact angle from MD simulations directly and in a computationally efficient way. This algorithm segregates the droplet molecules from the vapor molecules using Mahalanobis distance (MND) technique. Then the density is smeared onto a 2D grid using 4th order B-spline interpolation function. The vapor liquid interface data is estimated from the grid using density filtering. With the interface data a circle is fitted using Landau method. The equation of this circle is solved for obtaining the contact angle. This procedure is repeated by rotating the droplet about the vertical axis. We ha...
Dynamic stresses induced in turbo-alternator shaft are important design considerations. It is cru... more Dynamic stresses induced in turbo-alternator shaft are important design considerations. It is crucial to understand the complex vibrational mechanisms experienced by a turbo-alternator shaft. In this paper a dynamic model of the turbo-alternator shaft including support bearings is formulated. The equation of motion of the rotating turbo-alternator shaft is derived using Lagrangian formulation with finite-element method. The turbo-alternator shaft components with circular cross-section are discretized into a number of finite beam elements with 6 degrees of freedom at each node. The model accounts for the gyroscopic and centrifugal effects. Explicit expressions of the finite element inertia coupling and axial stiffening matrices are derived using a consistent mass formulation. The model is converted to state space equations for the easiness of solving. Thus developed model is integrated into a computational scheme and the dynamic response of the shaft is studied at different loading c...
Sphere fitting is a common problem in almost all science and engineering disciplines. Most of met... more Sphere fitting is a common problem in almost all science and engineering disciplines. Most of methods available are iterative in behavior. This involves fitting of the parameters in a least square sense or in a geometric sense. Here we extend the methods of Thomas Chan and Landau who fitted the 2D data using circle. This work closely resemble their work in redefining the error estimate and solving the sphere fitting problem exactly. The solutions for center and radius of the sphere can be found exactly and the equations can be hard coded for high performance. We have also shown some comparison with other popular methods and how this method behaves.
The Journal of Physical Chemistry Letters, 2015
A novel surface-heating algorithm for water is developed for molecular dynamics simulations. The ... more A novel surface-heating algorithm for water is developed for molecular dynamics simulations. The validated algorithm can simulate the transient behavior of the evaporation of water when heated from a surface, which has been lacking in the literature. In this work, the algorithm is used to study the evaporation of water droplets on a platinum surface at different temperatures. The resulting contact angles of the droplets are compared to existing theoretical, numerical, and experimental studies. The evaporation profile along the droplet's radius and height is deduced along with the temperature gradient within the drop, and the evaporation behavior conforms to the Kelvin−Clapeyron theory. The algorithm captures the realistic differential thermal gradient in water heated at the surface and is promising for studying various heating/cooling problems, such as thin film evaporation, Leidenfrost effect, and so forth. The simplicity of the algorithm allows it to be easily extended to other surfaces and integrated into various molecular simulation software and user codes.
Journal of Biomolecular Structure and Dynamics, 1995
Cytochrome P450cam is capable of reductively dehalogenating several chlorinated alkanes at low, b... more Cytochrome P450cam is capable of reductively dehalogenating several chlorinated alkanes at low, but measurable, rates. In previous investigations of structure-function relationships in this enzyme using molecular dynamics simulations, we noticed that 1,1,1-trichloroethane (TCA) exhibits a very high degree of mobility in the active site due to its smaller molecular volume relative to the native substrate, camphor(1,2). Several amino acid sidechains
International Journal of Control, 2001
Langmuir
Evaporation studies of water using classical molecular dynamics simulations are largely limited d... more Evaporation studies of water using classical molecular dynamics simulations are largely limited due to their high computational expense. This study addresses that issue by developing coarse-grained molecular dynamics models based on Morse potential. Models are optimized based on multi-temperature and at room temperature using machine learning techniques like genetic algorithm, Nelder-Mead algorithm, and Strength Pareto Evolutionary Algorithm. The multi-temperature based model named as Morse-D is found to be more accurate than single temperature model in representing the water properties at higher temperatures. Using this Morse-D water model, evaporation from hydrophilic nanopores with pore diameter varying from 2 to 5 is studied. Our results show that the critical diameter to initiate continuous evaporation at nanopores lies between 3 and 4. A maximum heat flux of 21.3 / 2 is observed for a pore diameter of 4.5 and a maximum mass flow rate of 16.2 / for a pore diameter of 5. The observed heat flux is an order of magnitude times larger than the currently reported values from experiments in the literature for water, which indicates that we need to focus on nanoscale evaporation to enhance the critical heat flux.
In this work, a tool for estimating the contact angle from the molecular dynamics simulations is ... more In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial phy...
This investigation explores a novel path-planning and optimization strategy for multiple cooperat... more This investigation explores a novel path-planning and optimization strategy for multiple cooperative robotic agents, applied in a fully observable and dynamically changing obstacle field. Current dynamic path planning strategies employ static algorithms operating over incremental time-steps. We propose a cooperative multi-agent (CMA) based algorithm, based on natural flocking of animals, using vector operations. It is preferred over more common graph search algorithms like A* as it can be easily applied for dynamic environments. CMA algorithm executes obstacle avoidance using static potential fields around obstacles, that scale based on relative motion. Optimization strategies including interpolation and Bezier curves are applied to the algorithm. To validate effectiveness, CMA algorithm is compared with A* using static obstacles due to lack of equivalent algorithms for dynamic environments. CMA performed comparably to A* with difference ranging from -0.2% to 1.3%. CMA algorithm is ...
Microsystem Technologies-micro-and Nanosystems-information Storage and Processing Systems, Jul 4, 2020
This article details the analysis of the thermo-hydraulic performance of a single-phase MEMS Heat... more This article details the analysis of the thermo-hydraulic performance of a single-phase MEMS Heat sink with pin fins integrated in micro channels. Circular pin-fins with in-line arrangement are considered in this study. The influence of operating and geometric parameters on the performance, (thermal resistance and pressure drop) are studied; the parameters considered include microchannel hydraulic diameter, microchannel spacing, substrate material, pin-fin pitch, and Reynolds number. Additionally, the performance is quantified in terms of a Figure of Merit (FOM) which is the product of normalized thermal resistance and normalized pressure drop. The thermal resistance of heat sink with pin-fin integrated in micro channels is lower than that in heat sinks without pin-fins irrespective of the Reynolds number. On the other hand, the pressure drop associated with heat sink with pin-fins integrated in microchannel is higher than that in heat sinks without pin-fins for all Reynolds number. Also, increase in hydraulic diameter leads to reduction in thermal resistance and increase in pressure drop for a specific Reynolds number. On the other hand, reduction in microchannel spacing leads to reduction in thermal resistance for a specific Reynolds number; the pressure drop is independent of the microchannel spacing. With regards to the influence of substrate material, the thermal resistance decreased with increase in thermal conductivity; the pressure drop is not influenced by changes in substrate material.
Journal of Molecular Modeling, 2018
Studies suggest that patients with deep vein thrombosis and diabetes often have hypercoagulable b... more Studies suggest that patients with deep vein thrombosis and diabetes often have hypercoagulable blood plasma, leading to a higher risk of thromboembolism formation through the rupture of blood clots, which may lead to stroke and death. Despite many advances in the field of blood clot formation and thrombosis, the influence of mechanical properties of fibrin in the formation of thromboembolisms in platelet-poor plasma is poorly understood. In this paper, we combine the concepts of reactive molecular dynamics and coarse-grained molecular modeling to predict the complex network formation of fibrin clots and the branching of fibrin monomers. The 340-kDa fibrinogen molecule was converted into a coarse-grained molecule with nine beads, and using our customized reactive potentials, we simulated the formation and polymerization process of a fibrin clot. The results show that higher concentrations of thrombin result in higher branch-point formation in the fibrin clot structure. Our results a...
Supplementary_Information_-_CATH for Glucose Concentration Affects Fibrin Clot Structure and Morp... more Supplementary_Information_-_CATH for Glucose Concentration Affects Fibrin Clot Structure and Morphology as Evidenced by Fluorescence Imaging and Molecular Simulations by Jacob E. Hood, Sumith Yesudasan, and Rodney D. Averett in Clinical and Applied Thrombosis/Hemostasis
ArXiv, 2021
Weak passwords and availability of supercomputers to password crackers make the financial institu... more Weak passwords and availability of supercomputers to password crackers make the financial institutions and businesses at stake. This calls for use of strong passwords and multi factor authentication for secure transactions. Remembering a long and complex password by humans is a daunting task and mnemonic has helped to mitigate this situation to an extent. This paper discusses creating and using long random password and storing them securely using a hybrid strategy of hash-encryption method. The hash function uses a mnemonic password based on the hotel names and other characteristics like room number, floor number and breakfast meal preferences to generate the encryption key. The random strong password can be then encrypted using the key and stored safely. A computer program named Hector is developed which demonstrates these steps and can be used to generate and store the passwords.
In this work, we investigate the pressure and density characteristics of water film when simulate... more In this work, we investigate the pressure and density characteristics of water film when simulated using the emerging technique called many body dissipative particle dynamics method. This work also layout the methodology of estimating local pressure from LAMMPS simulation using Harasima scheme. Using the triangular shaped cloud interpolation function, pressure and density are estimated at local bins and compared with the experimental database. Our results show good agreement for the molecular dynamics results of the argon system, while the many body dissipative particle model fails to simulate the water properties at room temperature. In its current form, the many body dissipative particle method cannot be used for accurate liquid vapor interfacial simulations and heat transfer studies.
Blood clots occur in the human body when they are required to prevent bleeding. In pathological s... more Blood clots occur in the human body when they are required to prevent bleeding. In pathological states such as diabetes and sickle cell disease, blood clots can also form undesirably due to hypercoagulable plasma conditions. With the continued effort in developing fibrin therapies for potential life-saving solutions, more mechanical modeling is needed to understand the properties of fibrin structures with inclusions. In this study, a fibrin matrix embedded with magnetic micro particles (MMPs) was subjected to a magnetic field to determine the magnitude of the required force to create plastic deformation within the fibrin clot. Using finite element (FE) analysis, we estimated the magnetic force from an electromagnet at a sample space located approximately 3 cm away from the coil center. This electromagnetic force coupled with gravity was applied on a fibrin mechanical system with MMPs to calculate the stresses and displacements. Using appropriate coil parameters, it was determined that application of a magnetic field of 730 A/m on the fibrin surface was necessary to achieve an electromagnetic force of 36 nN (to engender plastic deformation).
arXiv: Biological Physics, 2018
The multiscale behavior of the individual fibrin fibers and fibrin clots is modeled by coupling a... more The multiscale behavior of the individual fibrin fibers and fibrin clots is modeled by coupling atomistic simulation data and microscopic experimental data. We propose a protofibril element made up of nonlinear spring network, constructed based on the molecular simulation and atomic force microscopy results to simulate the force extension behavior of fibrin fibers. This new network model also accounts for the complex interaction of protofibrils with each other, effect of presence of solvent, Coulombic attraction and other binding forces. The network model is applied to simulate the force extension behavior of single fibrin fiber from atomic force microscopy experiments and shows good agreement. Thus validated fibrin fiber network model is then combined with a modified version of Arruda-Boyce eight chain model to estimate the force extension behavior of continuum level fibrin clot, which shows very good correlation. The results show that this network model is able to predict the beha...
In this paper, we introduce a simple yet powerful and working version of the molecular dynamics c... more In this paper, we introduce a simple yet powerful and working version of the molecular dynamics code using the Python 3.9 language. The code contents are published in the link given in the appendix 1. The structure and components of the program is given in detail using flowcharts and code snippets. The program consists of major features like velocity verlet integrator, thermostats, COM removal, input and output modules, virial, pressure, and other thermodynamic quantities estimation etc. The author believes that this program will be helpful to graduate students who perform research in molecular dynamics simulations who intend to write their own code instead of the sophisticated open source packages.
This paper investigates the improvement in solar energy collection and conversion using Al2O3-Wat... more This paper investigates the improvement in solar energy collection and conversion using Al2O3-Water nanofluids in a solar flat plate collector (SFPC). The efficiency of a solar flat plate collector using water as the fluid medium is analyzed experimentally and theoretically. For theoretical analysis, a mathematical model in MATLAB is used to simulate and is validated by the experimental results. To enhance the solar energy collection and conversion efficiency of the SFPC, Al2O3-Water nanofluid was selected as the fluid medium. The nanofluid properties like density, specific heat capacity, thermal conductivity and viscosity are analyzed and compared for several models of Al2O3-Water nanofluids and the best model was selected to modify the simulation. Effect of particle diameter in the nanofluid was found to be marginal on the nanofluid properties. The optimum volume concentration of the nanofluid was found to be 4% giving an efficiency increase of 7.78% in the SFPC over the use of wa...
Journal of Molecular Graphics and Modelling, 2018
Coupling of statistical properties from atomistic simulations to continuum is essential to model ... more Coupling of statistical properties from atomistic simulations to continuum is essential to model many multi-scale phenomena. Often, the system under consideration will be homogeneous in twodimensions (2-D). But due to the existing coupling methods, the property estimation takes place in three-dimensions (3-D) and then averaged to 2-D, which is computationally expensive due to the 3-D convolutions. A direct 2-D pressure or stress estimation model is lacking in literature. In this work, we develop a direct 2-D pressure field estimation method which is much faster than 3-D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor. This formulation will enable the study of 2-D fundamental phenomena like passive liquid flows in microlayer, as well as facilitate the coupling of atomistic and continuum simulations with reduced computational cost.
ASME 2015 13th International Conference on Nanochannels, Microchannels, and Minichannels, 2015
It is important to study contact angle of a liquid on a solid surface to understand its wetting p... more It is important to study contact angle of a liquid on a solid surface to understand its wetting properties, capillarity and surface interaction energy. While performing transient molecular dynamics (MD) simulations it requires calculating the time evolution of contact angle. This is a tedious effort to do manually or with image processing algorithms. In this work we propose a new algorithm to estimate contact angle from MD simulations directly and in a computationally efficient way. This algorithm segregates the droplet molecules from the vapor molecules using Mahalanobis distance (MND) technique. Then the density is smeared onto a 2D grid using 4th order B-spline interpolation function. The vapor liquid interface data is estimated from the grid using density filtering. With the interface data a circle is fitted using Landau method. The equation of this circle is solved for obtaining the contact angle. This procedure is repeated by rotating the droplet about the vertical axis. We ha...
Dynamic stresses induced in turbo-alternator shaft are important design considerations. It is cru... more Dynamic stresses induced in turbo-alternator shaft are important design considerations. It is crucial to understand the complex vibrational mechanisms experienced by a turbo-alternator shaft. In this paper a dynamic model of the turbo-alternator shaft including support bearings is formulated. The equation of motion of the rotating turbo-alternator shaft is derived using Lagrangian formulation with finite-element method. The turbo-alternator shaft components with circular cross-section are discretized into a number of finite beam elements with 6 degrees of freedom at each node. The model accounts for the gyroscopic and centrifugal effects. Explicit expressions of the finite element inertia coupling and axial stiffening matrices are derived using a consistent mass formulation. The model is converted to state space equations for the easiness of solving. Thus developed model is integrated into a computational scheme and the dynamic response of the shaft is studied at different loading c...
Sphere fitting is a common problem in almost all science and engineering disciplines. Most of met... more Sphere fitting is a common problem in almost all science and engineering disciplines. Most of methods available are iterative in behavior. This involves fitting of the parameters in a least square sense or in a geometric sense. Here we extend the methods of Thomas Chan and Landau who fitted the 2D data using circle. This work closely resemble their work in redefining the error estimate and solving the sphere fitting problem exactly. The solutions for center and radius of the sphere can be found exactly and the equations can be hard coded for high performance. We have also shown some comparison with other popular methods and how this method behaves.
The Journal of Physical Chemistry Letters, 2015
A novel surface-heating algorithm for water is developed for molecular dynamics simulations. The ... more A novel surface-heating algorithm for water is developed for molecular dynamics simulations. The validated algorithm can simulate the transient behavior of the evaporation of water when heated from a surface, which has been lacking in the literature. In this work, the algorithm is used to study the evaporation of water droplets on a platinum surface at different temperatures. The resulting contact angles of the droplets are compared to existing theoretical, numerical, and experimental studies. The evaporation profile along the droplet's radius and height is deduced along with the temperature gradient within the drop, and the evaporation behavior conforms to the Kelvin−Clapeyron theory. The algorithm captures the realistic differential thermal gradient in water heated at the surface and is promising for studying various heating/cooling problems, such as thin film evaporation, Leidenfrost effect, and so forth. The simplicity of the algorithm allows it to be easily extended to other surfaces and integrated into various molecular simulation software and user codes.
Journal of Biomolecular Structure and Dynamics, 1995
Cytochrome P450cam is capable of reductively dehalogenating several chlorinated alkanes at low, b... more Cytochrome P450cam is capable of reductively dehalogenating several chlorinated alkanes at low, but measurable, rates. In previous investigations of structure-function relationships in this enzyme using molecular dynamics simulations, we noticed that 1,1,1-trichloroethane (TCA) exhibits a very high degree of mobility in the active site due to its smaller molecular volume relative to the native substrate, camphor(1,2). Several amino acid sidechains
International Journal of Control, 2001
Langmuir
Evaporation studies of water using classical molecular dynamics simulations are largely limited d... more Evaporation studies of water using classical molecular dynamics simulations are largely limited due to their high computational expense. This study addresses that issue by developing coarse-grained molecular dynamics models based on Morse potential. Models are optimized based on multi-temperature and at room temperature using machine learning techniques like genetic algorithm, Nelder-Mead algorithm, and Strength Pareto Evolutionary Algorithm. The multi-temperature based model named as Morse-D is found to be more accurate than single temperature model in representing the water properties at higher temperatures. Using this Morse-D water model, evaporation from hydrophilic nanopores with pore diameter varying from 2 to 5 is studied. Our results show that the critical diameter to initiate continuous evaporation at nanopores lies between 3 and 4. A maximum heat flux of 21.3 / 2 is observed for a pore diameter of 4.5 and a maximum mass flow rate of 16.2 / for a pore diameter of 5. The observed heat flux is an order of magnitude times larger than the currently reported values from experiments in the literature for water, which indicates that we need to focus on nanoscale evaporation to enhance the critical heat flux.
In this work, a tool for estimating the contact angle from the molecular dynamics simulations is ... more In this work, a tool for estimating the contact angle from the molecular dynamics simulations is developed and presented. The tool (Achilles) can detect water droplet on hydrophobic and hydrophilic surfaces. The tool can reconstruct the droplets broken across the periodic boundaries. Further a neighbor density based accurate filter is used to find the droplet liquid vapor interface and a circle is fitted using it after removing the dense layers of water next to solid surface. This fitted circle is solved for contact angle and results are outputted in the form of graphical images and text. The entire content of the internal computations of the tool is broken down into 4 phases and users can monitor the outcomes at every phase through output images. The tool is tested using sample molecular dynamics results of water droplet on hydrophobic and hydrophilic surfaces. We believe this tool can be a good addition to the molecular dynamics simulation community who work on the interfacial phy...
This investigation explores a novel path-planning and optimization strategy for multiple cooperat... more This investigation explores a novel path-planning and optimization strategy for multiple cooperative robotic agents, applied in a fully observable and dynamically changing obstacle field. Current dynamic path planning strategies employ static algorithms operating over incremental time-steps. We propose a cooperative multi-agent (CMA) based algorithm, based on natural flocking of animals, using vector operations. It is preferred over more common graph search algorithms like A* as it can be easily applied for dynamic environments. CMA algorithm executes obstacle avoidance using static potential fields around obstacles, that scale based on relative motion. Optimization strategies including interpolation and Bezier curves are applied to the algorithm. To validate effectiveness, CMA algorithm is compared with A* using static obstacles due to lack of equivalent algorithms for dynamic environments. CMA performed comparably to A* with difference ranging from -0.2% to 1.3%. CMA algorithm is ...
Studies suggests that patients with deep vein thrombosis and diabetes often have hyper coagulable... more Studies suggests that patients with deep vein thrombosis and diabetes often have hyper coagulable blood plasma leading to higher chances of forming thromboembolisms by the rupture of blood clots, which may lead to stroke and death. Despite the advances in the field of blood clot formation and lysis research, the change in mechanical properties and its implication into the formation of thromboembolisms in platelet poor plasma is poorly understood. In this paper, we present a new computational method to simulate fibrin clot formation using molecular simulations. With an effective combination of reactive molecular dynamics concept and coarse graining principle, we have utilized the reactive coarse grain molecular dynamics to predict the complex network formation of fibrin clots and the branching of the fibrins. The heavy 340 kDa fibrinogen is converted into a simple spring-bead coarse grain system with 9 beads, and using our customized reactive potentials, we simulated the formation of the fibrin clot. Thus, formed fibrin clot agrees with the experimental results qualitatively, and to our best knowledge this is the first kind of molecular polymerization study of fibrin clot which can lead to improve our understanding about blood clot formation and its relationship with mechanical properties