FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2896638470> ?p ?o ?g. }

• W2896638470 endingPage "150901" @default.
• W2896638470 startingPage "150901" @default.
• W2896638470 abstract "The statistical analysis of molecular dynamics simulations requires dimensionality reduction techniques, which yield a low-dimensional set of collective variables (CVs) {xi} = x that in some sense describe the essential dynamics of the system. Considering the distribution P(x) of the CVs, the primal goal of a statistical analysis is to detect the characteristic features of P(x), in particular, its maxima and their connection paths. This is because these features characterize the low-energy regions and the energy barriers of the corresponding free energy landscape ΔG(x) = −kBT ln P(x), and therefore amount to the metastable states and transition regions of the system. In this perspective, we outline a systematic strategy to identify CVs and metastable states, which subsequently can be employed to construct a Langevin or a Markov state model of the dynamics. In particular, we account for the still limited sampling typically achieved by molecular dynamics simulations, which in practice seriously limits the applicability of theories (e.g., assuming ergodicity) and black-box software tools (e.g., using redundant input coordinates). We show that it is essential to use internal (rather than Cartesian) input coordinates, employ dimensionality reduction methods that avoid rescaling errors (such as principal component analysis), and perform density based (rather than k-means-type) clustering. Finally, we briefly discuss a machine learning approach to dimensionality reduction, which highlights the essential internal coordinates of a system and may reveal hidden reaction mechanisms." @default.
• W2896638470 created "2018-10-26" @default.
• W2896638470 creator A5048297803 @default.
• W2896638470 creator A5078308961 @default.
• W2896638470 date "2018-10-21" @default.
• W2896638470 modified "2023-10-11" @default.
• W2896638470 title "Perspective: Identification of collective variables and metastable states of protein dynamics" @default.
• W2896638470 cites W1742512077 @default.
• W2896638470 cites W185137928 @default.
• W2896638470 cites W1964066268 @default.
• W2896638470 cites W1966111577 @default.
• W2896638470 cites W1966743338 @default.
• W2896638470 cites W1969256423 @default.
• W2896638470 cites W1969723894 @default.
• W2896638470 cites W1975310895 @default.
• W2896638470 cites W1977875643 @default.
• W2896638470 cites W1980782498 @default.
• W2896638470 cites W1985591276 @default.
• W2896638470 cites W1987774535 @default.
• W2896638470 cites W1988220126 @default.
• W2896638470 cites W1990387274 @default.
• W2896638470 cites W1999933791 @default.
• W2896638470 cites W2001141328 @default.
• W2896638470 cites W2006554089 @default.
• W2896638470 cites W2011119007 @default.
• W2896638470 cites W2011430131 @default.
• W2896638470 cites W2013638340 @default.
• W2896638470 cites W2014095962 @default.
• W2896638470 cites W2015656580 @default.
• W2896638470 cites W2016267980 @default.
• W2896638470 cites W2018312454 @default.
• W2896638470 cites W2021214016 @default.
• W2896638470 cites W2022239151 @default.
• W2896638470 cites W2025899185 @default.
• W2896638470 cites W2028130802 @default.
• W2896638470 cites W2032398506 @default.
• W2896638470 cites W2033120570 @default.
• W2896638470 cites W2033745076 @default.
• W2896638470 cites W2044201287 @default.
• W2896638470 cites W2051116535 @default.
• W2896638470 cites W2053186076 @default.
• W2896638470 cites W2053348581 @default.
• W2896638470 cites W2056211671 @default.
• W2896638470 cites W2056786025 @default.
• W2896638470 cites W2058868284 @default.
• W2896638470 cites W2058971275 @default.
• W2896638470 cites W2062105576 @default.
• W2896638470 cites W2063021109 @default.
• W2896638470 cites W2064556178 @default.
• W2896638470 cites W2068726834 @default.
• W2896638470 cites W2072290134 @default.
• W2896638470 cites W2075243501 @default.
• W2896638470 cites W2075460992 @default.
• W2896638470 cites W2077412035 @default.
• W2896638470 cites W2080664920 @default.
• W2896638470 cites W2083895330 @default.
• W2896638470 cites W2085213650 @default.
• W2896638470 cites W2086003265 @default.
• W2896638470 cites W2090264443 @default.
• W2896638470 cites W2091966043 @default.
• W2896638470 cites W2094795801 @default.
• W2896638470 cites W2096125044 @default.
• W2896638470 cites W2103014607 @default.
• W2896638470 cites W2109102515 @default.
• W2896638470 cites W2110497788 @default.
• W2896638470 cites W2123182960 @default.
• W2896638470 cites W2130390906 @default.
• W2896638470 cites W2132589721 @default.
• W2896638470 cites W2136567909 @default.
• W2896638470 cites W2137295153 @default.
• W2896638470 cites W2145326890 @default.
• W2896638470 cites W2146411229 @default.
• W2896638470 cites W2149655632 @default.
• W2896638470 cites W2157792819 @default.
• W2896638470 cites W2158323088 @default.
• W2896638470 cites W2158476854 @default.
• W2896638470 cites W2160862046 @default.
• W2896638470 cites W2161168724 @default.
• W2896638470 cites W2162141320 @default.
• W2896638470 cites W2165414288 @default.
• W2896638470 cites W2165434144 @default.
• W2896638470 cites W2165835468 @default.
• W2896638470 cites W2216435628 @default.
• W2896638470 cites W2226825552 @default.
• W2896638470 cites W2252661420 @default.
• W2896638470 cites W2283818235 @default.
• W2896638470 cites W2313374938 @default.
• W2896638470 cites W2315297180 @default.
• W2896638470 cites W2316045758 @default.
• W2896638470 cites W2317421918 @default.
• W2896638470 cites W2322273605 @default.
• W2896638470 cites W2325642794 @default.
• W2896638470 cites W2326170450 @default.
• W2896638470 cites W2328938694 @default.
• W2896638470 cites W2330733193 @default.
• W2896638470 cites W2334841042 @default.
• W2896638470 cites W2341303730 @default.
• W2896638470 cites W2346320169 @default.

• next