Do Lattice Protein Simulations Exhibit Self-Organized Criticality?

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. The goal of my research is to better understand the protein folding process through a lattice HP model simulation with a Monte-Carlo based algorithm. Specifically, amino acids in the chain at each time step are allowed to fold to certain locations according to two main criteria: folds must maintain bond length and should be thermally and energetically favorable. This simulation will then be used to examine whether the folding process can be viewed through the lens of self-organized criticality (SOC). In particular, I am interested in whether there are features of the folding process that are independent of the size of the protein. The power law behavior found in SOC systems was not clearly found for the protein lengths studied. Further studies of the model should be investigated

Computational Studies of Protein Folding

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. The goal of our research is to better understand the protein folding process. Using MATLAB, we created an algorithm that models the folding process via a Monte Carlo time step approach. Specifically, amino acids in the chain at each time step are allowed to fold to certain locations according to a set of rules. These rules are based on two main criteria: folds must maintain bond length and should be thermally and energetically favorable. One central goal of our research is to examine whether the folding process can be viewed through the lens of self-organized criticality. In particular we are interested in whether there are features of the folding process that are independent of the size of the protein

Does Protein Folding Exhibit Self-Organized Criticality?

Proteins are known to fold into tertiary structures that determine their functionality in living organisms. By understanding the general features of this folding process, that are independent of specific proteins, folding can be better understood. Self-organized critical systems exhibit behavior that scales with system size. In this project, I wrote a simulation of a simplistic three-dimensional cubic lattice protein model. The model consisted of only two different types of amino acids, one being hydrophobic and the other hydrophilic, known as the HP model. To identify self-organized criticality in proteins, there must be clear signs of power law behavior in the folding process. Initial results show indications of self-organized criticality in protein folding; however, there is also a sign of limitation with the computational model used

Role of Contacts in Capacitance Measurements of Solar Cells

The electronic properties of low cost, thin-film solar cells are complicated by the non-ideal nature of the semiconductor layers. Typically, the fundamental electronic properties of such materials are evaluated using current-voltage and capacitance-voltage measurements. However, in these devices, it is common for the back contact to be non-ohmic. We are exploring the impact of such a back contact on the outcome of standard capacitance-based characterization techniques. We compare computer models of capacitance response with measurements of simple model electronic circuits and of solar cell devices

Using Automation to Understand Sustainable Design Trade-Offs and to Promote Environmental Sustainability in the Early Design Phase

Sustainable product design is becoming an important component of the development of consumer products. Currently there are limited design resources to aid in the creation of environmentally sustainable products. The purpose of this research is to theorize a new method for integrating sustainable design knowledge into the early design phase of new products and processes. A novel organized search tree--consisting of sustainable product design guidelines, empirical design knowledge, international design regulations and preliminary consumer preference information--is constructed to enable application of sustainable design knowledge before and during concept generation. To further facilitate its application, this search tree is embedded in an easy-to-use web-based application called the GREEn Quiz (Guidelines and Regulations for Early design for the Environment). The quiz provides users with weighted questions pertaining to the design or redesign of a product concept, with a list of possible pre-generated responses to choose from. As a designer progresses through the quiz, user responses are compiled and weighted, and a final report that displays the top ten design attributes contributing to the eventual environmental impact of the product are provided to the user. Accompanied by the top ten list, is a list of design decisions that can be used to better help inform the designer to make improvements that can make the product more sustainable. To further assist designers in understanding the impact of their design decisions, a preliminary investigation into life cycle estimation is conducted by training an artificial neural network on 37 different consumer products. The results of this work found that the design method facilitates designers of varied experience to increase the number of environmentally conscience design decisions made in the concept generation process. It was also found that a neural network can be used to learn valuable correlations between product attributes and life cycle data (which is promising for life cycle impact estimation), but further work into increasing the capability of the neural network approach is required before this data can be used to inform the weights used in the GREEn Quiz. Without new environmentally conscious methods similar to the current method, it will continue to be challenging to design eco-friendly products, and the impact of consumable products will continue to be unsustainable

Computational Studies of Protein Folding

Proteins are known to fold to tertiary structures that determine the functionality of the protein in living organisms. The goal of our research is to better understand the protein folding process and to see if protein folding is a self-organized critical process. There are many different examples of self-organized criticality in nature, such as sand piles and earthquakes. Using MATLAB, we create an algorithm that models the folding process via a Monte Carlo time step approach. Specifically, amino acids in the chain at each time step are allowed to fold to certain locations according to a set of rules. We hope to observe whether or not the protein folding process exhibits features that are independent of the protein\u27s size (a typical trait of self-organized criticality)

Duality of Time

This sculpture was created as part of the Linfield College course Introduction to Studio, taught by Totem Shriver.https://digitalcommons.linfield.edu/avcstud_toothpick/1018/thumbnail.jp