Vishakha Sharma, PhD

Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biochemical pathways is a computationally intensive challenge. Traditional tools, such as ordinary differential equations, partial differential equations, stochastic master equations, and Gillespie type methods, are all limited either by their modeling fidelity or computational efficiency or both. In this work, we present a scalable computational framework based on… Show more

Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biochemical pathways is a computationally intensive challenge. Traditional tools, such as ordinary differential equations, partial differential equations, stochastic master equations, and Gillespie type methods, are all limited either by their modeling fidelity or computational efficiency or both. In this work, we present a scalable computational framework based on modeling biochemical reactions in explicit 3D space, that is suitable for studying the behavior of large and complex biological pathways. The framework is designed to exploit parallelism and scalability offered by commodity massively parallel processors such as the graphics processing units (GPUs) and other parallel computing platforms. The reaction modeling in 3D space is aimed at enhancing the realism of the model compared to traditional modeling tools and framework. We introduce the Parallel Select algorithm that is key to breaking the sequential bottleneck limiting the performance of most other tools designed to study biochemical interactions. The algorithm is designed to be computationally tractable, handle hundreds of interacting chemical species and millions of independent agents by considering all-particle interactions within the system. We also present an implementation of the framework on the popular graphics processing units and apply it to the simulation study of JAK-STAT Signal Transduction Pathway. The computational framework will offer a deeper insight into various biological processes within the cell and help us observe key events as they unfold in space and time. This will advance the current state-of-the-art in simulation study of large scale biological systems and also enable the realistic simulation study of macro-biological cultures, where inter-cellular interactions are prevalent. Show less

The problem of counterfeiting is of particular concern in the Department of Defense (DoD) supply chain, where it may lead to lack of assurance of reliability of complex systems, and it may endanger operational performance and safety. In this paper, we present a computational approach to studying complex socio-technical systems relevant to the analysis of the effects of counterfeit parts in the military supply chain. We illustrate our technique with the case study of Magellan GPS 315. Using the… Show more

The problem of counterfeiting is of particular concern in the Department of Defense (DoD) supply chain, where it may lead to lack of assurance of reliability of complex systems, and it may endanger operational performance and safety. In this paper, we present a computational approach to studying complex socio-technical systems relevant to the analysis of the effects of counterfeit parts in the military supply chain. We illustrate our technique with the case study of Magellan GPS 315. Using the Stochastic Pi Machine (SPiM), we build a stochastic agent-based computational model to study the effects of counterfeit components in the performance of a complex multi-component system. We discuss the combinatorial complexity of the agent-based model. We implement a visualization of the system. Finally, statistical tests are performed to analyze the difference in multi-component systems' performance relative to the proportions verified and counterfeit components.

We believe that computational models like this can contribute to identifying counterfeiting and studying its effects in the military supply chain. Show less

We define BioScape^L, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that
entities have programmable locations. The programmer can specify a particular location where to
place an entity, or a location relative to the current location of the entity. The motivation for the extension comes from the need to describe the evolution of populations of biochemical species in space, while keeping a sufficiently high level description, so that phenomena like diffusion… Show more

We define BioScape^L, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that
entities have programmable locations. The programmer can specify a particular location where to
place an entity, or a location relative to the current location of the entity. The motivation for the extension comes from the need to describe the evolution of populations of biochemical species in space, while keeping a sufficiently high level description, so that phenomena like diffusion, collision, and confinement can remain part of the semantics of the calculus. Combined with the random diffusion movement inherited from BioScape, programmable locations allow us to capture the assemblies of configurations of polymers, oligomers, and complexes such as microtubules or actin filaments.

Further new aspects of BioScape^L include random translation and scaling. Random translation
is instrumental in describing the location of new entities relative to the old ones. For example, when
a cell secretes a hydronium ion, the ion should be placed at a given distance from the originating cell, but in a random direction. Additionally, scaling allows us to capture at a high level events such as division and growth; for example, daughter cells after mitosis have half the size of the mother cell. Show less

We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in… Show more

We design BioScape, a concurrent language for the stochastic simulation of biological and bio-materials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections.

The novel aspects of BioScape include syntactic primitives to declare the scope in space where species can move, diffusion rate, shape, and reaction distance, and an operational semantics that deals with the specifics of 3D locations, verifying reaction distance, and featuring random movement. We define a translation from BioScape to 3π and prove its soundness with respect to the operational semantics. Show less

The JAK (Janus kinase)-STAT (Signal transducer and activator of transcription) signal transduction pathway is a cascade of downstream cellular events initiated from outside of the cell through the cell surface to the DNA in the nucleus, causing transcription. The conventional modeling approach for signal transduction pathways involves solving ordinary differential equations (ODEs). We study here a computational alternative. We build two models of 46 reactions in the JAK-STAT pathway and compare… Show more

The JAK (Janus kinase)-STAT (Signal transducer and activator of transcription) signal transduction pathway is a cascade of downstream cellular events initiated from outside of the cell through the cell surface to the DNA in the nucleus, causing transcription. The conventional modeling approach for signal transduction pathways involves solving ordinary differential equations (ODEs). We study here a computational alternative. We build two models of 46 reactions in the JAK-STAT pathway and compare the results. We implement a deterministic mathematical model using the ODEs solver COPASI, and we build a stochastic computational model using the Stochastic Pi Machine (SPiM).

Since dysregulation in the functionality of JAK-STAT pathway results in immune deficiency syndrome and cancers, like lymphomas, leukemia and breast cancer, we believe that models like this have the potential to contribute to cancer research. Show less

Traditionally biomaterials development consists of designing a surface and testing its properties experimentally. This trial-and-error approach is limited because of the resources and time needed to sample a representative number of configurations in a combinatorially complex scenario. Therefore, computational modeling is of significant importance in identifying best antibacterial materials to prevent and treat implant related biofilm infections.

In this paper we focus on bifunctional… Show more

Traditionally biomaterials development consists of designing a surface and testing its properties experimentally. This trial-and-error approach is limited because of the resources and time needed to sample a representative number of configurations in a combinatorially complex scenario. Therefore, computational modeling is of significant importance in identifying best antibacterial materials to prevent and treat implant related biofilm infections.

In this paper we focus on bifunctional surface with polymer brushes and Pluronic-Lysozyme conjugates developed by Henk Busscher's group in Groningen, The Netherlands. The bifunctional brushes act as anti-adhesive due to the unmodified polymer brushes and antibacterial, because of the Pluronic-Lysozyme conjugates. They developed and studied three different surfaces with varying proportions of antibacterial and anti-adhesive properties. In order to aid the development of optimal bifunctional surfaces, we build a three dimensional computational model using BioScape, an agent-based modeling and simulation language developed by Compagnoni's group at Stevens. We model two different experimental phases: adhesion and growth. We use the results of experiments on two surfaces as training data, and we validate our model by reproducing the experimental results from the third surface. The resulting model is able to simulate varying configurations of surface coatings both at adhesion and growth phases at a fraction of the time necessary to perform in-vitro experiments.

The output of the model not only plots populations over time, but it also produces 3D-rendered videos of bacteria-surface interactions enhancing the visualization of the system's behavior. Show less

BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in treating and preventing biofilm infections. As its predecessor, SPiM, BioScape has a sequential semantics based on Gillespie's algorithm, and its implementation does not scale beyond 1000 agents. However, in order to model larger and more realistic systems, a… Show more

BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in treating and preventing biofilm infections. As its predecessor, SPiM, BioScape has a sequential semantics based on Gillespie's algorithm, and its implementation does not scale beyond 1000 agents. However, in order to model larger and more realistic systems, a semantics that may take advantage of the new multi-core and GPU architectures is needed. This motivates the introduction of parallel semantics, which is the contribution of this paper: Parallel BioScape, an extension with fully parallel semantics. Show less

Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biological systems is a computationally intensive challenge. We present a GPU based simulation framework in a reactive environment in 3D space, along with the modeling language, BioScape, in order to describe various biological processes. We also present an efficient computational framework to study the interactions enabled by the massively parallel processing… Show more

Biological systems encompass complexity that far surpasses many artificial systems. Modeling and simulation of large and complex biological systems is a computationally intensive challenge. We present a GPU based simulation framework in a reactive environment in 3D space, along with the modeling language, BioScape, in order to describe various biological processes. We also present an efficient computational framework to study the interactions enabled by the massively parallel processing capability of the GPUs. Our driving example is a bio-triggered drug delivery system for infection-resistant medical implants. The modeling and simulation framework presented here will help in identifying biological targets and materials to treat biomaterials associated bacterial infections. The computational framework will offer a deeper insight into various biological processes compared to traditional modeling via implicit differential equations, and help us observe the key events as they unfold. Show less