scholarly journals Efficient Search for Energetically Favorable Molecular Conformations against Metastable States via Gray-Box Optimization

Author(s):  
Kei Terayama ◽  
Masato Sumita ◽  
Michio Katouda ◽  
Koji Tsuda ◽  
Yasushi Okuno
1981 ◽  
Vol 42 (C4) ◽  
pp. C4-395-C4-398 ◽  
Author(s):  
M. Wautelet ◽  
R. Andrew ◽  
M. Failly-Lovato ◽  
L. D. Laude

Author(s):  
Vishnu Sharma ◽  
Vijay Singh Rathore ◽  
Chandikaditya Kumawat

Software reuse can improve software quality with the reducing cost and development time. Systematic reuse plan enhances cohesion and reduces coupling for better testability and maintainability. Software reuse approach can be adopted at the highest extent if relevant software components can be easily searched, adapted and integrated into new system. Large software industries hold their own well managed component libraries containing well tested software component with the project category based classification .Access to these repositories are very limited. Software reuse is facing so many problems and still not so popular. This is due to issues of general access, efficient search and adoption of software component. This paper propose a framework which resolves all of the above issues with providing easy access to components, efficient incremental semantics based search, repository management, versioning of components.


2020 ◽  
Author(s):  
Anna Nowakowska ◽  
Alasdair D F Clarke ◽  
Jessica Christie ◽  
Josephine Reuther ◽  
Amelia R. Hunt

We measured the efficiency of 30 participants as they searched through simple line segment stimuli and through a set of complex icons. We observed a dramatic shift from highly variable, and mostly inefficient, strategies with the line segments, to uniformly efficient search behaviour with the icons. These results demonstrate that changing what may initially appear to be irrelevant, surface-level details of the task can lead to large changes in measured behaviour, and that visual primitives are not always representative of more complex objects.


2021 ◽  
Vol 103 (2) ◽  
Author(s):  
V. A. Dzuba ◽  
Saleh O. Allehabi ◽  
V. V. Flambaum ◽  
Jiguang Li ◽  
S. Schiller

2021 ◽  
Vol 184 (1) ◽  
Author(s):  
Gianmarco Bet ◽  
Vanessa Jacquier ◽  
Francesca R. Nardi

AbstractWe consider the problem of metastability for stochastic dynamics with exponentially small transition probabilities in the low temperature limit. We generalize previous model-independent results in several directions. First, we give an estimate of the mixing time of the dynamics in terms of the maximal stability level. Second, assuming the dynamics is reversible, we give an estimate of the associated spectral gap. Third, we give precise asymptotics for the expected transition time from any metastable state to the stable state using potential-theoretic techniques. We do this in a general reversible setting where two or more metastable states are allowed and some of them may even be degenerate. This generalizes previous results that hold for a series of only two metastable states. We then focus on a specific Probabilistic Cellular Automata (PCA) with configuration space $${\mathcal {X}}=\{-1,+1\}^\varLambda $$ X = { - 1 , + 1 } Λ where $$\varLambda \subset {\mathbb {Z}}^2$$ Λ ⊂ Z 2 is a finite box with periodic boundary conditions. We apply our model-independent results to find sharp estimates for the expected transition time from any metastable state in $$\{\underline{-1}, {\underline{c}}^o,{\underline{c}}^e\}$$ { - 1 ̲ , c ̲ o , c ̲ e } to the stable state $$\underline{+1}$$ + 1 ̲ . Here $${\underline{c}}^o,{\underline{c}}^e$$ c ̲ o , c ̲ e denote the odd and the even chessboard respectively. To do this, we identify rigorously the metastable states by giving explicit upper bounds on the stability level of every other configuration. We rely on these estimates to prove a recurrence property of the dynamics, which is a cornerstone of the pathwise approach to metastability.


Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3974
Author(s):  
A. Daryl Ariawan ◽  
Flora Mansour ◽  
Nicole Richardson ◽  
Mohan Bhadbhade ◽  
Junming Ho ◽  
...  

Histone deacetylase enzymes (HDACs) are potential targets for the treatment of cancer and other diseases, but it is challenging to design isoform-selective agents. In this work, we created new analogs of two established but non-selective HDAC inhibitors. We decorated the central linker chains of the molecules with specifically positioned fluorine atoms in order to control the molecular conformations. The fluorinated analogs were screened against a panel of 11 HDAC isoforms, and minor differences in isoform selectivity patterns were observed.


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