Electronic System-Level Synthesis Methodologies
Summary (2 min read)
Introduction
- Understanding the mechanism of phase transformations of protein aqueous solutions is important for several applications in materials science and biotechnology.
- 5,6 However, a sound scientific basis of the thermodynamic behavior of protein aqueous solutions is still missing.
- The chemical potential of the protein component is changed by the concentration of the additive in two ways.
- The corresponding experimental results have been interpreted by using microscopic models based on preferential hydration (or binding),9 DLVO (Derjaguin-Landau-VerweyOverbeek) interactions,14 depletion interactions (or crowding),15 and Donnan effects.16 24.
- Yet, they have been qualitatively successful in describing the effect of PEG molecular weight on the thermodynamic behavior of protein solutions.
Thermodynamic Perturbation Theory
- The authors will now outline a thermodynamic perturbation theory that will be used to describe the liquid-liquid phase transition for the protein-polymer-buffer system.
- The contribution of polymer to the translational entropy of the system is represented by c2 ln(c2/e), whereas c2(∂f̂ex/∂c2) is the first term of a series expansion describing the effect of polymer concentration on the excess free energy, f̂ex.
- Furthermore, this approach also can be used to describe the presence of protein/polymer partitioning in the two coexisting liquid phases.
- Yet, most of their experimental results are far from critical conditions and will be analyzed using eq 5 not eq 6.
- For pure excluded-volume interactions, eq 4 predicts that, as the polymer concentration increases, (∂µ̂1/∂c1)T,µ̂2 decreases and can be made to reach zero.
Materials and Methods
- Bovine serum albumin (BSA) was purchased from Sigma (purity 99%).
- The concentration of PEG1450 in the samples was calculated by using the mass of PEG and the total volume of the solution.
- The total volume was calculated from the sample mass using the corresponding specific volume, i.e., 0.735 mL/g for the protein,42 0.84 mL/g for PEG,24 and 1.000 mL/g for the buffer (the buffer density was measured using a DMA40 Mettler-Paar density meter) as in previous work.
- The temperature reported for the onset of LLPS was Tph ) (Tcloud + Tclear)/2 as recommended in previous work.
- The protein concentration in each phase was determined by UV absorption.
Results
- The chosen buffer for the studies on the BSA-PEG1450 mixtures was a 0.1 M sodium acetate aqueous solution at pH 5.2.
- This also suggests that the amount of PEG1450 required to induce LLPS at this pH is close to the minimum.
- To characterize protein-protein interactions in the proteinbuffer binary system, the authors determine the value of its second virial coefficient, B2, at 298.15 K. Similar results were also obtained for γ-crystallin-PEG aqueous mixtures.
- The authors thus expect that the proteinconcentrate phases may still contain small amounts (∼10%) of the protein-dilute phase.
Discussion
- The thermodynamic behavior of the BSA-PEG1450-buffer system can be examined by applying the above-described thermodynamic perturbation theory to their experimental results.
- The phase boundary is then computed by repeating this procedure for several values of Tph and µ̂2.
- For this system, LLPS with a lower critical point is also observed when the temperature is increased above 363 K, consistent with previous results.
- 54 Thus the effect of BSA is to move this phase boundary toward lower temperatures.
Summary and Conclusions
- The authors have examined the thermodynamic behavior of the BSAPEG1450-buffer system using LLPS measurements.
- For this system, the authors have experimentally determined the effect of PEG concentration on the LLPS temperature and protein/PEG partitioning in the two coexisting phases.
- The authors results were interpreted using a thermodynamic perturbation theory.
- The authors believe that the parallel examination of these two thermodynamic properties is a valuable tool for verifying the reliability of existing models and for developing more accurate ones.
- Finally, the authors have shown that protein-PEG-buffer mixtures can also exhibit two distinct liquid-liquid phase transitions.
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"Electronic System-Level Synthesis M..." refers background in this paper
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"Electronic System-Level Synthesis M..." refers background in this paper
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Q2. What are the future works mentioned in the paper "Electronic system-level synthesis methodologies" ?
Nevertheless, no single approach currently provides a complete solution, and further research in many areas is required. In the future, the authors plan to investigate such interoperability issues using combinations of different tools presented in this paper. On the other hand, based on the common concepts and principles identified in this classification, it should be possible to define interfaces such that different point tools can be combined into an overall ESL design environment. Last, but not least, the authors would like to thank the reviewers for their helpful comments and suggestions in making this paper a much stronger contribution.
Q3. What can be used to test values of internal variables and data in the input channels?
constant methods called guards (e.g., check) can be used to test values of internal variables and data in the input channels.
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Finding a good application-to-architecture mapping is carried out during a two-phase automatic architecture exploration step consisting of static and dynamic (i.e., simulative) exploration methods using a TAPM MoP.
Q5. How long did the prototyping work take?
Due to the highly automated design flow of Daedalus, all DSE and prototyping work was performed in only a short amount of time, five days in total.
Q6. What are examples of performance models for different classes of granularity?
Examples of simulation-based MoPs for different classes of timing granularity are cycle-accurate performance models (CAPMs), instruction-set-accurate performance models (ISAPMs), or task-accurate performance models (TAPMs) [12].
Q7. How can lower level flows be supplied?
Lower level flows can be supplied either in the form of corresponding synthesis tools or by providing predesigned intellectual property (IP) components to be plugged into the system architecture.
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The FSM controlling the communication behavior of the SysteMoC actor checks for available input data (e.g., #i1 ≥ 1) and available space on the output channels (e.g., #o1 ≥ 1) to store results.
Q9. What is the main observation that can be made from Fig. 1?
An important observation that can be made from Fig. 1 is that, at the RT level, hardware and software worlds unite again, both feeding into (traditional) logic design processes down to the final manufacturing output.
Q10. Why are many streaming applications not modeled as static dataflow graphs?
Due to the complexity of many streaming applications, they often cannot be modeled as static dataflow graphs [30], [31], where consumption and production rates are known at compile time.
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These components include a variety of programmable processors, dedicated hardwired IP cores, memories, and interconnects, thereby allowing the implementation of a wide range of heterogeneous MPSoC platforms.
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Q14. What is the last step of the proposed ESL design flow?
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