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You searched for +publisher:"Virginia Tech" +contributor:("Onufriev, Alexey V."). Showing records 1 – 12 of 12 total matches.

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Virginia Tech

1. Daga, Mayank. Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems.

Degree: MS, Computer Science, 2011, Virginia Tech

 The emergence of scientific applications embedded with multiple modes of parallelism has made heterogeneous computing systems indispensable in high performance computing. The popularity of such… (more)

Subjects/Keywords: molecular modeling; performance evaluation; optimization; OpenCL; CUDA; GPU; multicore CPU

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APA (6th Edition):

Daga, M. (2011). Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/32535

Chicago Manual of Style (16th Edition):

Daga, Mayank. “Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems.” 2011. Masters Thesis, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/32535.

MLA Handbook (7th Edition):

Daga, Mayank. “Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems.” 2011. Web. 22 Jan 2021.

Vancouver:

Daga M. Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems. [Internet] [Masters thesis]. Virginia Tech; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/32535.

Council of Science Editors:

Daga M. Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems. [Masters Thesis]. Virginia Tech; 2011. Available from: http://hdl.handle.net/10919/32535


Virginia Tech

2. Anandakrishnan, Ramamoorthi. Speeding up electrostatic computations for molecular dynamics.

Degree: PhD, Computer Science and Applications, 2011, Virginia Tech

 Molecular dynamics (MD) simulations are routinely used to study the structure and function of biological molecules. However the accuracy and duration of these simulations are… (more)

Subjects/Keywords: statistical mechanics; biomolecular electrostatics; molecular dynamics

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APA (6th Edition):

Anandakrishnan, R. (2011). Speeding up electrostatic computations for molecular dynamics. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/40262

Chicago Manual of Style (16th Edition):

Anandakrishnan, Ramamoorthi. “Speeding up electrostatic computations for molecular dynamics.” 2011. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/40262.

MLA Handbook (7th Edition):

Anandakrishnan, Ramamoorthi. “Speeding up electrostatic computations for molecular dynamics.” 2011. Web. 22 Jan 2021.

Vancouver:

Anandakrishnan R. Speeding up electrostatic computations for molecular dynamics. [Internet] [Doctoral dissertation]. Virginia Tech; 2011. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/40262.

Council of Science Editors:

Anandakrishnan R. Speeding up electrostatic computations for molecular dynamics. [Doctoral Dissertation]. Virginia Tech; 2011. Available from: http://hdl.handle.net/10919/40262


Virginia Tech

3. Aguilar Huacan, Boris Abner. Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling.

Degree: PhD, Computer Science and Applications, 2014, Virginia Tech

 Biomolecular Modeling is playing an important role in many practical applications such as biotechnology and structure-based drug design. One of the essential requirements of Biomolecular… (more)

Subjects/Keywords: Molecular Modeling; Implicit solvents; Generalized Born Model

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APA (6th Edition):

Aguilar Huacan, B. A. (2014). Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/64409

Chicago Manual of Style (16th Edition):

Aguilar Huacan, Boris Abner. “Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling.” 2014. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/64409.

MLA Handbook (7th Edition):

Aguilar Huacan, Boris Abner. “Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling.” 2014. Web. 22 Jan 2021.

Vancouver:

Aguilar Huacan BA. Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling. [Internet] [Doctoral dissertation]. Virginia Tech; 2014. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/64409.

Council of Science Editors:

Aguilar Huacan BA. Improving of the accuracy and efficiency of implicit solvent models in Biomolecular Modeling. [Doctoral Dissertation]. Virginia Tech; 2014. Available from: http://hdl.handle.net/10919/64409

4. Izadi, Saeed. Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber.

Degree: PhD, Engineering Mechanics, 2016, Virginia Tech

 Atomistic modeling and simulation methods enable a modern molecular approach to bio-medical research. Issues addressed range from structure-function relationships to structure-based drug design. The ability… (more)

Subjects/Keywords: Molecular Modeling; Explicit Solvent Model; Force Field; Implicit Solvent Model; Point Charge Approximation; Multipole Moments; Electrostatics; Water Models; Multi-scale Models

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APA (6th Edition):

Izadi, S. (2016). Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/81539

Chicago Manual of Style (16th Edition):

Izadi, Saeed. “Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber.” 2016. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/81539.

MLA Handbook (7th Edition):

Izadi, Saeed. “Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber.” 2016. Web. 22 Jan 2021.

Vancouver:

Izadi S. Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber. [Internet] [Doctoral dissertation]. Virginia Tech; 2016. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/81539.

Council of Science Editors:

Izadi S. Optimal Point Charge Approximation: from 3-Atom Water Molecule to Million-Atom Chromatin Fiber. [Doctoral Dissertation]. Virginia Tech; 2016. Available from: http://hdl.handle.net/10919/81539


Virginia Tech

5. Grothaus, Gregory. Biologically-Interpretable Disease Classification Based on Gene Expression Data.

Degree: MS, Computer Science, 2005, Virginia Tech

 Classification of tissues and diseases based on gene expression data is a powerful application of DNA microarrays. Many popular classifiers like support vector machines, nearest-neighbour… (more)

Subjects/Keywords: Classification; Biclustering; Gene Expression; Microarrays

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APA (6th Edition):

Grothaus, G. (2005). Biologically-Interpretable Disease Classification Based on Gene Expression Data. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/33288

Chicago Manual of Style (16th Edition):

Grothaus, Gregory. “Biologically-Interpretable Disease Classification Based on Gene Expression Data.” 2005. Masters Thesis, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/33288.

MLA Handbook (7th Edition):

Grothaus, Gregory. “Biologically-Interpretable Disease Classification Based on Gene Expression Data.” 2005. Web. 22 Jan 2021.

Vancouver:

Grothaus G. Biologically-Interpretable Disease Classification Based on Gene Expression Data. [Internet] [Masters thesis]. Virginia Tech; 2005. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/33288.

Council of Science Editors:

Grothaus G. Biologically-Interpretable Disease Classification Based on Gene Expression Data. [Masters Thesis]. Virginia Tech; 2005. Available from: http://hdl.handle.net/10919/33288


Virginia Tech

6. Bhattacharjee, Puranjoy. Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency.

Degree: MS, Computer Science, 2009, Virginia Tech

 We have explored correlations between the measured efficiency of the RNAi process and several computed signatures that characterize equilibrium secondary structure of the partic- ipating… (more)

Subjects/Keywords: RNAi efficiency; RNA interference(RNAi); RNAi equilibrium thermodynamics; Support Vector Machine; RNA secondary structure

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APA (6th Edition):

Bhattacharjee, P. (2009). Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/34643

Chicago Manual of Style (16th Edition):

Bhattacharjee, Puranjoy. “Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency.” 2009. Masters Thesis, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/34643.

MLA Handbook (7th Edition):

Bhattacharjee, Puranjoy. “Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency.” 2009. Web. 22 Jan 2021.

Vancouver:

Bhattacharjee P. Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency. [Internet] [Masters thesis]. Virginia Tech; 2009. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/34643.

Council of Science Editors:

Bhattacharjee P. Correlation Between Computed Equilibrium Secondary Structure Free Energy and siRNA Efficiency. [Masters Thesis]. Virginia Tech; 2009. Available from: http://hdl.handle.net/10919/34643


Virginia Tech

7. Gordon, John Carroll. A new computationally facile approximation of electrostatic potential suitable for macromolecules.

Degree: MS, Computer Science, 2007, Virginia Tech

 The electrostatic properties of a molecule are often essential in determining its behavior; as such, the ability to approximate these electrostatic potentials computationally is often… (more)

Subjects/Keywords: Virus; Macromolecule; GEM; APLB; Poisson-Boltzmann; Electrostatic potential

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APA (6th Edition):

Gordon, J. C. (2007). A new computationally facile approximation of electrostatic potential suitable for macromolecules. (Masters Thesis). Virginia Tech. Retrieved from http://hdl.handle.net/10919/31216

Chicago Manual of Style (16th Edition):

Gordon, John Carroll. “A new computationally facile approximation of electrostatic potential suitable for macromolecules.” 2007. Masters Thesis, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/31216.

MLA Handbook (7th Edition):

Gordon, John Carroll. “A new computationally facile approximation of electrostatic potential suitable for macromolecules.” 2007. Web. 22 Jan 2021.

Vancouver:

Gordon JC. A new computationally facile approximation of electrostatic potential suitable for macromolecules. [Internet] [Masters thesis]. Virginia Tech; 2007. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/31216.

Council of Science Editors:

Gordon JC. A new computationally facile approximation of electrostatic potential suitable for macromolecules. [Masters Thesis]. Virginia Tech; 2007. Available from: http://hdl.handle.net/10919/31216


Virginia Tech

8. Fenley, Andrew Townsend. Simple Physical Approaches to Complex Biological Systems.

Degree: PhD, Physics, 2010, Virginia Tech

 Properly representing the principle physical interactions of complex biological systems is paramount for building powerful, yet simple models. As an in depth look into different… (more)

Subjects/Keywords: post-translational modification; small RNA; quorum sensing; Poisson-Boltzmann; nucleosome

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APA (6th Edition):

Fenley, A. T. (2010). Simple Physical Approaches to Complex Biological Systems. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/38819

Chicago Manual of Style (16th Edition):

Fenley, Andrew Townsend. “Simple Physical Approaches to Complex Biological Systems.” 2010. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/38819.

MLA Handbook (7th Edition):

Fenley, Andrew Townsend. “Simple Physical Approaches to Complex Biological Systems.” 2010. Web. 22 Jan 2021.

Vancouver:

Fenley AT. Simple Physical Approaches to Complex Biological Systems. [Internet] [Doctoral dissertation]. Virginia Tech; 2010. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/38819.

Council of Science Editors:

Fenley AT. Simple Physical Approaches to Complex Biological Systems. [Doctoral Dissertation]. Virginia Tech; 2010. Available from: http://hdl.handle.net/10919/38819


Virginia Tech

9. Ruscio, Jory Zmuda. Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution.

Degree: PhD, Genetics, Bioinformatics, and Computational Biology, 2007, Virginia Tech

 While experiments provide valuable information about biological molecules, current technology cannot yet monitor atomic fluctuations at relevant time scales. Theoretical computational simulations are able to… (more)

Subjects/Keywords: nucleosome core particle; myoglobin; beta-glucosidases; molecular dynamics

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APA (6th Edition):

Ruscio, J. Z. (2007). Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/27219

Chicago Manual of Style (16th Edition):

Ruscio, Jory Zmuda. “Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution.” 2007. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/27219.

MLA Handbook (7th Edition):

Ruscio, Jory Zmuda. “Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution.” 2007. Web. 22 Jan 2021.

Vancouver:

Ruscio JZ. Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution. [Internet] [Doctoral dissertation]. Virginia Tech; 2007. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/27219.

Council of Science Editors:

Ruscio JZ. Molecular Modeling: Elucidation of Structure/Function Relationships of Proteins and DNA at the Atomic Resolution. [Doctoral Dissertation]. Virginia Tech; 2007. Available from: http://hdl.handle.net/10919/27219


Virginia Tech

10. Sirk, Timothy Wayne. A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological Membranes.

Degree: PhD, Mechanical Engineering, 2009, Virginia Tech

 Molecular dynamics simulations were performed to study the interactions of bioactive catechins and theaflavins commonly found in tea with lipid bilayers, as a model for… (more)

Subjects/Keywords: Bilayer; Molecular Dynamics; Polyphenol; Theaflavin; Catechin

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APA (6th Edition):

Sirk, T. W. (2009). A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological Membranes. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/26946

Chicago Manual of Style (16th Edition):

Sirk, Timothy Wayne. “A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological Membranes.” 2009. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/26946.

MLA Handbook (7th Edition):

Sirk, Timothy Wayne. “A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological Membranes.” 2009. Web. 22 Jan 2021.

Vancouver:

Sirk TW. A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological Membranes. [Internet] [Doctoral dissertation]. Virginia Tech; 2009. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/26946.

Council of Science Editors:

Sirk TW. A Molecular Dynamics Study on the Interaction of Tea Catechins and Theaflavins with Biological Membranes. [Doctoral Dissertation]. Virginia Tech; 2009. Available from: http://hdl.handle.net/10919/26946


Virginia Tech

11. Dharmarajan, Lakshmi. Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases.

Degree: PhD, Genetics, Bioinformatics, and Computational Biology, 2010, Virginia Tech

 Phosphoenolpyruvate carboxykinase (PEPCK) and phosphoenolpyruvate carboxylase (Pepc) are two important CO₂-fixation enzymes which share a similar reaction mechanism. Both operate through a lid-gated active site… (more)

Subjects/Keywords: phosphoenolpyruvate; structure-function; active-site lid; inhibition; PEP-Mn2+ distance; anion-quadrupole interaction

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APA (6th Edition):

Dharmarajan, L. (2010). Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/77040

Chicago Manual of Style (16th Edition):

Dharmarajan, Lakshmi. “Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases.” 2010. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/77040.

MLA Handbook (7th Edition):

Dharmarajan, Lakshmi. “Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases.” 2010. Web. 22 Jan 2021.

Vancouver:

Dharmarajan L. Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases. [Internet] [Doctoral dissertation]. Virginia Tech; 2010. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/77040.

Council of Science Editors:

Dharmarajan L. Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases. [Doctoral Dissertation]. Virginia Tech; 2010. Available from: http://hdl.handle.net/10919/77040


Virginia Tech

12. Rajasimha, Harsha Karur. Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation.

Degree: PhD, Genetics, Bioinformatics, and Computational Biology, 2007, Virginia Tech

 MtDNA mutations in mammalian cells are implicated in cellular ageing and encephalomyopathies, although mechanisms involved are not completely understood. The mitochondrial genetic bottleneck has puzzled… (more)

Subjects/Keywords: heteroplasmy; fusion; fission; blood; inheritance; model; morphology; mtDNA; stem cells; segregation; oogenesis; ageing; mutations

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APA (6th Edition):

Rajasimha, H. K. (2007). Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation. (Doctoral Dissertation). Virginia Tech. Retrieved from http://hdl.handle.net/10919/29961

Chicago Manual of Style (16th Edition):

Rajasimha, Harsha Karur. “Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation.” 2007. Doctoral Dissertation, Virginia Tech. Accessed January 22, 2021. http://hdl.handle.net/10919/29961.

MLA Handbook (7th Edition):

Rajasimha, Harsha Karur. “Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation.” 2007. Web. 22 Jan 2021.

Vancouver:

Rajasimha HK. Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation. [Internet] [Doctoral dissertation]. Virginia Tech; 2007. [cited 2021 Jan 22]. Available from: http://hdl.handle.net/10919/29961.

Council of Science Editors:

Rajasimha HK. Insights Into Mitochondrial Genetic and Morphologic Dynamics Gained by Stochastic Simulation. [Doctoral Dissertation]. Virginia Tech; 2007. Available from: http://hdl.handle.net/10919/29961

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