Browsing by Subject "Biopolymer"
Now showing 1 - 2 of 2
Results Per Page
Sort Options
Item Biopolymer Simulations: From Next-Generation Genomics to Consumer Products(2018-04) Li, XiaolanBiopolymers have many unique properties which play an essential and pervasive role in everyday life, thus making them attractive for engineering applications. Understand- ing how the particular properties of biopolymers give rise to important applications in technology remains a long-standing challenge. Although biopolymers can have different chemistries, they share some common physical properties: high molecular weights, stiff backbones, and complex internal structures. Computer simulation, therefore, plays quite an important role since it provides a way to study a generic model that, by changing the parameters appearing in the model, permits studying a wide variety of biopolymers. Specifically, we focus on two such biopolymers: DNA and methylcellulose. This thesis focuses on studying the universal properties of the two aforementioned biopolymers using novel molecular simulation techniques. DNA attracts particularly strong interest not only because of its fascinating double- helix structure but also because DNA carries biological information. Genomic mapping is emerging as a new technology to provide information about large-scale genomic structural variations. In this context, the conformation and properties of the linearized DNA are only beginning to be understood. With a Monte Carlo chain growth method known as pruned-enriched Rosenbluth method, we explore the force-extension relationship of stretched DNA. In this scenario, external forces and confinement are two fundamental and complementary aspects. We begin by stretching a single DNA in free solution. This allows separation of restrictions imposed by forces from that by walls. This work shows that the thickness of DNA plays an important role in the force-extension behavior. The key outcome is a new expression that approximates the force-extension behavior with about 5% relative error for all range of forces. We then analyze slit-confined DNA stretched by an external force. This work predicted a new regime in the force-extension behavior that features a mixed effect of both sensible DNA volume and sensible wall effects. We anticipate such a complete description of the force-extension of DNA will prove useful for the design of new genomic mapping technologies. The dissertation also involves another biopolymer, methylcellulose, which has an extremely wide range of commercial uses. Methylcellulose is thermoresponsive polymer that undergoes a morphological transition at elevated temperature, forming uniform diameter fibrils. However, mechanisms behind the solution-gel transition are poorly understood. Following the computational studies by Huang et al. [1], we apply Langevin dynamics simulations to a coarse-grained model that produces collapsed ring-like structures in dilute solution with a radius close to the fibrils observed in experiments. We show that the competition between the dihedral potential and self-attraction causes these collapsed states to undergo a rapid conformational change, which helps the chain to avoid kinetic traps by permitting a transition between collapsed states. We expect our findings from computational studies of biopolymers will not only provide a deep understanding of semiflexible polymer physics but also inspire novel engineering applications relying on the properties of biopolymers.Item DNA confined in nanochannels and nanoslits(2014-05) Tree, DouglasIt has become increasingly apparent in recent years that next-generation sequencing (NGS) has a blind spot for large scale genomic variation, which is crucial for understanding the genotype-phenotype relationship. Genomic mapping methods attempt to overcome the weakesses of NGS by providing a coarse-grained map of the distances between restriction sites to aid in sequence assembly. From such methods, one hopes to realize fast and inexpensive de novo sequencing of human and plant genomes.One of the most promising methods for genomic mapping involves placing DNA inside a device only a few dozen nanometers wide called a nanochannel. A nanochannel stretches the DNA so that the distance between fluorescently labeled restriction sites can be measured en route to obtaining an accurate genome map. Unfortunately for those who wish to design devices, the physics of how DNA stretches when confined in a nanochannel is still an active area of research. Indeed, despite decades old theories from polymer physics regarding weakly and strongly stretched polymers, seminal experiments in the mid-2000s have gone unexplained until very recently.With a goal of creating a realistic engineering model of DNA in nanochannels, this dissertation addresses a number of important outstanding research topics in this area. We first discuss the physics of dilute solutions of DNA in free solution, which show distinctive behavior due to the stiff nature of the polymer. We then turn our attention to the equilibrium regimes of confined DNA and explore the effects of stiff chains and weak excluded volume on the confinement free energy and polymer extension. We also examine dynamic properties such as the diffusion coefficient and the characteristic relaxation time. Finally, we discuss a sister problem related to DNA confined in nanoslits, which shares much of the same physics as DNA confined in channels.Having done this, we find ourselves with a well-parameterized wormlike chain model that is remarkably accurate in describing the behavior of DNA in confinement. As such, it appears that researchers may proceed with the rational design of nanochannel mapping devices using this model.