Gene Transcription Modeling within a Random and Tethered Environment

Senior Project submitted to The Division of Science, Mathematics and Computing of Bard College

Utilization of Finite Element Analysis Techniques for Adolescent Idiopathic Scoliosis Surgical Planning

Adolescent Idiopathic Scoliosis, a three-dimensional deformity of the thoracolumbar spine, affects approximately 1-3% of patients ages 10-18. Surgical correction and treatment of the spinal column is a costly and high-risk task that is consistently complicated by factors such as patient-specific spinal deformities, curve flexibility, and surgeon experience. The following dissertation utilizes finite element analysis to develop a cost-effective, building-block approach by which surgical procedures and kinematic evaluations may be investigated. All studies conducted are based off a volumetric, thoracolumbar finite element (FE) model developed from computer-aided design (CAD) anatomy whose components are kinematically validated with in-vitro data. Spinal ligament stiffness properties derived from the literature are compared for kinematic assessment of a thoracic functional spinal unit (FSU) and benchmarked with available in-vitro kinematic data. Once ligament stiffness properties were selected, load sharing among soft tissues (e.g., ligaments and intervertebral disc) within the same FSU is then assessed during individual steps of a posterior correction procedure commonly used on scoliosis patients. Finally, the entire thoracolumbar spine is utilized to mechanically induce a mild scoliosis profile through an iterative preload and growth procedure described by the Hueter-Volkmann law. The mild scoliosis model is then kinematically compared with an asymptomatic counterpart. The thoracic deformation exhibited in the mild scoliosis model compared well with available CT datasets. Key findings of the studies confirm the importance of appropriately assigning spinal ligament properties with traditional toe and linear stiffness regimes to properly characterize thoracic spine FE models. Stiffness properties assigned within spinal FE models may also alter how intact ligaments and intervertebral discs respond to external loads during posterior correction procedures involving serial ligament removal, and thus can affect any desired post-surgical outcomes. Lastly, the thoracolumbar spine containing mild scoliosis experiences up to a 37% reduction in global range of motion compared to an asymptomatic spine, while also exhibiting larger decreases in segmental axial rotations at apical deformity levels. Future studies will address kinematic behavior of a severe scoliosis deformity and set the stage for column-based osseoligamentous load sharing assessments during surgical procedures

AUTOMATED NETWORK SECURITY WITH EXCEPTIONS USING SDN

Campus networks have recently experienced a proliferation of devices ranging from personal use devices (e.g. smartphones, laptops, tablets), to special-purpose network equipment (e.g. firewalls, network address translation boxes, network caches, load balancers, virtual private network servers, and authentication servers), as well as special-purpose systems (badge readers, IP phones, cameras, location trackers, etc.). To establish directives and regulations regarding the ways in which these heterogeneous systems are allowed to interact with each other and the network infrastructure, organizations typically appoint policy writing committees (PWCs) to create acceptable use policy (AUP) documents describing the rules and behavioral guidelines that all campus network interactions must abide by. While users are the audience for AUP documents produced by an organization\u27s PWC, network administrators are the responsible party enforcing the contents of such policies using low-level CLI instructions and configuration files that are typically difficult to understand and are almost impossible to show that they do, in fact, enforce the AUPs. In other words, mapping the contents of imprecise unstructured sentences into technical configurations is a challenging task that relies on the interpretation and expertise of the network operator carrying out the policy enforcement. Moreover, there are multiple places where policy enforcement can take place. For example, policies governing servers (e.g., web, mail, and file servers) are often encoded into the server\u27s configuration files. However, from a security perspective, conflating policy enforcement with server configuration is a dangerous practice because minor server misconfigurations could open up avenues for security exploits. On the other hand, policies that are enforced in the network tend to rarely change over time and are often based on one-size-fits-all policies that can severely limit the fast-paced dynamics of emerging research workflows found in campus networks. This dissertation addresses the above problems by leveraging recent advances in Software-Defined Networking (SDN) to support systems that enable novel in-network approaches developed to support an organization\u27s network security policies. Namely, we introduce PoLanCO, a human-readable yet technically-precise policy language that serves as a middle-ground between the imprecise statements found in AUPs and the technical low-level mechanisms used to implement them. Real-world examples show that PoLanCO is capable of implementing a wide range of policies found in campus networks. In addition, we also present the concept of Network Security Caps, an enforcement layer that separates server/device functionality from policy enforcement. A Network Security Cap intercepts packets coming from, and going to, servers and ensures policy compliance before allowing network devices to process packets using the traditional forwarding mechanisms. Lastly, we propose the on-demand security exceptions model to cope with the dynamics of emerging research workflows that are not suited for a one-size-fits-all security approach. In the proposed model, network users and providers establish trust relationships that can be used to temporarily bypass the policy compliance checks applied to general-purpose traffic -- typically by network appliances that perform Deep Packet Inspection, thereby creating network bottlenecks. We describe the components of a prototype exception system as well as experiments showing that through short-lived exceptions researchers can realize significant improvements for their special-purpose traffic

Effect of the Change of Inertial, Elastic and Dissipative Parameters on the Ride Comfort of a Road Vehicle

The comfort on a vehicle is of great interest as it is related with the driver perception and hence with ride safety conditions. Road infrastructure in Colombia presents unique characteristics; for that reason, there is interest in how road vehicles can be adapted to perform properly when they are subjected to the road conditions of the country. This work is centred on the study of the effect that a change on a set composed by vehicle’s inertial, elastic and dissipative parameters has on the ride comfort of a driver. The ride comfort of the driver is analysed in terms of exposition to vibrations induced by the road unevenness to the vehicle body. A computational approach is implemented, by means of a previously validated multibody model with seven degrees of freedom (DOF). Two road input configurations are considered, both of them generated by isolated bumps. The effect that a variation on several vehicle parameters has on the driver comfort was analysed using comfort indexes defined by the standard ISO 2631-1

Cell viscoelasticity is linked to fluctuations in cell biomass distributions.

The viscoelastic properties of mammalian cells can vary with biological state, such as during the epithelial-to-mesenchymal (EMT) transition in cancer, and therefore may serve as a useful physical biomarker. To characterize stiffness, conventional techniques use cell contact or invasive probes and as a result are low throughput, labor intensive, and limited by probe placement. Here, we show that measurements of biomass fluctuations in cells using quantitative phase imaging (QPI) provides a probe-free, contact-free method for quantifying changes in cell viscoelasticity. In particular, QPI measurements reveal a characteristic underdamped response of changes in cell biomass distributions versus time. The effective stiffness and viscosity values extracted from these oscillations in cell biomass distributions correlate with effective cell stiffness and viscosity measured by atomic force microscopy (AFM). This result is consistent for multiple cell lines with varying degrees of cytoskeleton disruption and during the EMT. Overall, our study demonstrates that QPI can reproducibly quantify cell viscoelasticity