3,913 research outputs found
Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability
Bryan S. Der, Ron Jacak, Brian Kuhlman, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, Andrew D. Ellington , Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, George Georgiou, Andrew D. Ellington, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of AmericaAleksandr E. Miklos, Andrew D. Ellington , Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of AmericaSergey Lyskov, Jeffrey J. Gray, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of AmericaBrian Kuhlman, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaReengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ~3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.This work was supported by the Defense Advanced Research Projects Agency (HR-0011-10-1-0052 to A.E.) and the Welch Foundation (F-1654 to A.E.), the National Institutes of Health grants GM073960 (B.K.) and R01-GM073151 (J.G. and S.L.), the Rosetta Commons (S.L.), the National Science Foundation graduate research fellowship (2009070950 to B.D.), the UNC Royster Society Pogue fellowship (B.D.), and National Institutes of Health grant T32GM008570 for the UNC Program in Molecular and Cellular Biophysics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Center for Systems and Synthetic BiologyCellular and Molecular BiologyApplied Research LaboratoriesEmail: [email protected]
Unfolding-Based Process Discovery
This paper presents a novel technique for process discovery. In contrast to
the current trend, which only considers an event log for discovering a process
model, we assume two additional inputs: an independence relation on the set of
logged activities, and a collection of negative traces. After deriving an
intermediate net unfolding from them, we perform a controlled folding giving
rise to a Petri net which contains both the input log and all
independence-equivalent traces arising from it. Remarkably, the derived Petri
net cannot execute any trace from the negative collection. The entire chain of
transformations is fully automated. A tool has been developed and experimental
results are provided that witness the significance of the contribution of this
paper.Comment: This is the unabridged version of a paper with the same title
appearead at the proceedings of ATVA 201
A Process Modelling Framework Based on Point Interval Temporal Logic with an Application to Modelling Patient Flows
This thesis considers an application of a temporal theory to describe and model the patient journey in the hospital accident and emergency (A&E) department. The aim is to introduce a generic but dynamic method applied to any setting, including healthcare. Constructing a consistent process model can be instrumental in streamlining healthcare issues. Current process modelling techniques used in healthcare such as flowcharts, unified modelling language activity diagram (UML AD), and business process modelling notation (BPMN) are intuitive and imprecise. They cannot fully capture the complexities of the types of activities and the full extent of temporal constraints to an extent where one could reason about the flows. Formal approaches such as Petri have also been reviewed to investigate their applicability to the healthcare domain to model processes.
Additionally, to schedule patient flows, current modelling standards do not offer any formal mechanism, so healthcare relies on critical path method (CPM) and program evaluation review technique (PERT), that also have limitations, i.e. finish-start barrier. It is imperative to specify the temporal constraints between the start and/or end of a process, e.g., the beginning of a process A precedes the start (or end) of a process B. However, these approaches failed to provide us with a mechanism for handling these temporal situations. If provided, a formal representation can assist in effective knowledge representation and quality enhancement concerning a process. Also, it would help in uncovering complexities of a system and assist in modelling it in a consistent way which is not possible with the existing modelling techniques.
The above issues are addressed in this thesis by proposing a framework that would provide a knowledge base to model patient flows for accurate representation based on point interval temporal logic (PITL) that treats point and interval as primitives. These objects would constitute the knowledge base for the formal description of a system. With the aid of the inference mechanism of the temporal theory presented here, exhaustive temporal constraints derived from the proposed axiomatic system’ components serves as a knowledge base.
The proposed methodological framework would adopt a model-theoretic approach in which a theory is developed and considered as a model while the corresponding instance is considered as its application. Using this approach would assist in identifying core components of the system and their precise operation representing a real-life domain deemed suitable to the process modelling issues specified in this thesis. Thus, I have evaluated the modelling standards for their most-used terminologies and constructs to identify their key components. It will also assist in the generalisation of the critical terms (of process modelling standards) based on their ontology. A set of generalised terms proposed would serve as an enumeration of the theory and subsume the core modelling elements of the process modelling standards. The catalogue presents a knowledge base for the business and healthcare domains, and its components are formally defined (semantics). Furthermore, a resolution theorem-proof is used to show the structural features of the theory (model) to establish it is sound and complete.
After establishing that the theory is sound and complete, the next step is to provide the instantiation of the theory. This is achieved by mapping the core components of the theory to their corresponding instances. Additionally, a formal graphical tool termed as point graph (PG) is used to visualise the cases of the proposed axiomatic system. PG facilitates in modelling, and scheduling patient flows and enables analysing existing models for possible inaccuracies and inconsistencies supported by a reasoning mechanism based on PITL. Following that, a transformation is developed to map the core modelling components of the standards into the extended PG (PG*) based on the semantics presented by the axiomatic system.
A real-life case (from the King’s College hospital accident and emergency (A&E) department’s trauma patient pathway) is considered to validate the framework. It is divided into three patient flows to depict the journey of a patient with significant trauma, arriving at A&E, undergoing a procedure and subsequently discharged. Their staff relied upon the UML-AD and BPMN to model the patient flows. An evaluation of their representation is presented to show the shortfalls of the modelling standards to model patient flows. The last step is to model these patient flows using the developed approach, which is supported by enhanced reasoning and scheduling
Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies
Grid is an infrastructure that involves the integrated and collaborative use
of computers, networks, databases and scientific instruments owned and managed
by multiple organizations. Grid applications often involve large amounts of
data and/or computing resources that require secure resource sharing across
organizational boundaries. This makes Grid application management and
deployment a complex undertaking. Grid middlewares provide users with seamless
computing ability and uniform access to resources in the heterogeneous Grid
environment. Several software toolkits and systems have been developed, most of
which are results of academic research projects, all over the world. This
chapter will focus on four of these middlewares--UNICORE, Globus, Legion and
Gridbus. It also presents our implementation of a resource broker for UNICORE
as this functionality was not supported in it. A comparison of these systems on
the basis of the architecture, implementation model and several other features
is included.Comment: 19 pages, 10 figure
Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices
Integrative biological simulations have a varied and controversial history in
the biological sciences. From computational models of organelles, cells, and
simple organisms, to physiological models of tissues, organ systems, and
ecosystems, a diverse array of biological systems have been the target of
large-scale computational modeling efforts. Nonetheless, these research agendas
have yet to prove decisively their value among the broader community of
theoretical and experimental biologists. In this commentary, we examine a range
of philosophical and practical issues relevant to understanding the potential
of integrative simulations. We discuss the role of theory and modeling in
different areas of physics and suggest that certain sub-disciplines of physics
provide useful cultural analogies for imagining the future role of simulations
in biological research. We examine philosophical issues related to modeling
which consistently arise in discussions about integrative simulations and
suggest a pragmatic viewpoint that balances a belief in philosophy with the
recognition of the relative infancy of our state of philosophical
understanding. Finally, we discuss community workflow and publication practices
to allow research to be readily discoverable and amenable to incorporation into
simulations. We argue that there are aligned incentives in widespread adoption
of practices which will both advance the needs of integrative simulation
efforts as well as other contemporary trends in the biological sciences,
ranging from open science and data sharing to improving reproducibility.Comment: 10 page
Molecular dynamics recipes for genome research
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect
Discovering Hierarchical Process Models: an Approach Based on Events Clustering
Process mining is a field of computer science that deals with discovery and
analysis of process models based on automatically generated event logs.
Currently, many companies use this technology for optimization and improving
their processes. However, a discovered process model may be too detailed,
sophisticated and difficult for experts to understand. In this paper, we
consider the problem of discovering a hierarchical business process model from
a low-level event log, i.e., the problem of automatic synthesis of more
readable and understandable process models based on information stored in event
logs of information systems.
Discovery of better structured and more readable process models is
intensively studied in the frame of process mining research from different
perspectives. In this paper, we present an algorithm for discovering
hierarchical process models represented as two-level workflow nets. The
algorithm is based on predefined event ilustering so that the cluster defines a
sub-process corresponding to a high-level transition at the top level of the
net. Unlike existing solutions, our algorithm does not impose restrictions on
the process control flow and allows for concurrency and iteration
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