Secondary Structures in Long Compact Polymers

Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform numerical calculations is generating a sufficiently large number of randomly sampled configurations. We present a Monte-Carlo algorithm which uniformly samples compact polymer configurations in an efficient manner allowing investigations of chains much longer than previously studied. Chain configurations generated by the algorithm are used to compute statistics of secondary structures in compact polymers. We determine the fraction of monomers participating in secondary structures, and show that it is self averaging in the long chain limit and strictly less than one. Comparison with results for lattice models of open polymer chains shows that compact chains are significantly more likely to form secondary structure.Comment: 14 pages, 14 figure

Airflow Model Testing to Determine the Distribution of Hot Gas Flow and O/F Ratio Across the Space Shuttle Main Engine Main Injector Assembly

Engine 0209, the certification engine for the new Phase 2+ Hot Gas Manifold (HGM), showed severe deterioration of the Main Combustion Chamber (MCC) liner during hot fire tests. One theory on the cause of the damage held that uneven local distribution of the fuel rich hot gas flow through the main injector assembly was producing regions of high oxidizer/fuel (O/F) ratio near the wall of the MCC liner. Airflow testing was proposed to measure the local hot gas flow rates through individual injector elements. The airflow tests were conducted using full scale, geometrically correct models of both the current Phase 2 and the new Phase 2+ HGMs. Different main injector flow shield configurations were tested for each HGM to ascertain their effect on the pressure levels and distribution of hot gas flow. Instrumentation located on the primary faceplate of the main injector measured hot gas flow through selected injector elements. These data were combined with information from the current space shuttle main engine (SSME) power balances to produce maps of pressure, hot gas flow rate, and O/F ratio near the main injector primary plate. The O/F distributions were compared for the different injector and HGM configurations

Converting Natural Language Phrases in Lambda Calculus to Generalized Constraint Language

This study explores one aspect of bridging Computing with Words with Natural Language Processing, to connect the extraction capabilities of Natural Language Processing with the inference capabilities of Computing with Words. Computing with Words uses Generalized Constraint Language to show the logical proposition of a given expression. A program was written to convert a logic-based lambda calculus representation of any English natural language expression into Generalized Constraint Language. The scope of this project is set to tagging parts of speech in simplistic expressions and is a foundation for expanding upon more complex lambda calculus expressions into Generalized Constraint Language. This program tags the parts of speech from the lambda calculus expression and outputs the Generalized Constraint Language of the expression, showing the constraint on an idea in the original sentence. This project establishes an entry point and is designed with further improvements and modifications in mind. The output from this project is useful in providing an understanding of bridging Natural Language Processing and Computing with Words, as the program creates a baseline of extracting parts of speech from a sentence to highlighting significant meaning of the given sentence.https://openriver.winona.edu/urc2019/1030/thumbnail.jp

Solvation vs. freezing in a heteropolymer globule

We address the response of a random heteropolymer to preferential solvation of certain monomer types at the globule-solvent interface. For each set of monomers that can comprise the molecule's surface, we represent the ensemble of allowed configurations by a Gaussian distribution of energy levels, whose mean and variance depend on the set's composition. Within such a random energy model, mean surface composition is proportional to solvation strength under most conditions. The breadth of this linear response regime arises from approximate statistical independence of surface and volume energies. For a diverse set of monomer types, the excess of solvophilic monomers at the surface is large only for very strong solvent preference, even in the ground state.Comment: 10 pages, 1 figur

Model checking

Automatic formal verification methods for finite-state systems, also known as model-checking, successfully reduce labor costs since they are mostly automatic. Model checkers explicitly or implicitly enumerate the reachable state space of a system, whose behavior is described implicitly, perhaps by a program or a collection of finite automata. Simple properties, such as mutual exclusion or absence of deadlock, can be checked by inspecting individual states. More complex properties, such as lack of starvation, require search for cycles in the state graph with particular properties. Specifications to be checked may consist of built-in properties, such as deadlock or 'unspecified receptions' of messages, another program or implicit description, to be compared with a simulation, bisimulation, or language inclusion relation, or an assertion in one of several temporal logics. Finite-state verification tools are beginning to have a significant impact in commercial designs. There are many success stories of verification tools finding bugs in protocols or hardware controllers. In some cases, these tools have been incorporated into design methodology. Research in finite-state verification has been advancing rapidly, and is showing no signs of slowing down. Recent results include probabilistic algorithms for verification, exploitation of symmetry and independent events, and the use symbolic representations for Boolean functions and systems of linear inequalities. One of the most exciting areas for further research is the combination of model-checking with theorem-proving methods

Blind protein structure prediction using accelerated free-energy simulations.

We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition

Unbiased sampling of globular lattice proteins in three dimensions

We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system

What's the Big IDeA?: Considerations for Implementing an Institutional Repository

Continually increasing journal costs have pushed libraries and research institutions to consider alternative forms of scholarly publication. One such form is that of the institutional digital repository (IR). As an early implementer of DSpace, an open-source institutional digital repository software product, IUPUI offers those just beginning to think about IRs an overview of issues such as: choosing a repository platform, staffing and technology needs, metadata and controlled vocabulary concerns, promotion, and time challenges. While the article outlines the process IUPUI followed to create its own IR, the piece is universalized to address the concerns of any new IR implementer