ライフサイエンスコーパス: free energy

1 exes that convert between different forms of free energy.

2 the most to the reduction in the activation free energy.

3 rfacial water while minimizing the torsional free energy.

4 oscopic particles is derived from the system free energy.

5 the number of competing polymorphs with low free energy.

6 ial due to its bulk-distortion and anchoring free energy.

7 he computed total is then the bulk hydration free energy.

8 ing multiple positions under the umbrella of free-energy.

9 ct of methylation on protein-protein binding free energies.

10 reveals that both the peptides populate high free energy aggregation-prone ([Formula: see text]) stat

11 ts are in agreement with our Ginzburg-Landau free energy analyses, showing that pressures tend to sta

12 A free-energy analysis reveals H(2) evolution is endergoni

13 Combination of the computed free energies and Abrahams' HB donating (alpha(2)(H)) an

14 We calculated reaction free energies and demonstrate the thermodynamic feasibil

15 The reaction free energies and free energy barriers are found to be s

16 uced current density), and monohydrogenation free energies and shows that a large span of aromatic pr

17 nding a conformation with both a low binding free energy and a small RMSD.

18 to the spectrin network, we obtain the total free energy and stresses in terms of invariants of shear

19 UBA has two polymorphs of almost equivalent free-energy and so is typically obtained as a polymorphi

20 xperiments show that protein-protein binding free energies are sensitive to the extent of methylation

21 Direct measurement of the free energies associated with each catalytic step correc

22 ions between particles arise to minimize the free energy associated with elastic distortions in the l

23 emical equilibrium and discuss the effective free energy at fixed pH.

24 We find that the free energy barrier between the CIP and SIP minima incre

25 eat significance, we are able to compare the free energy barrier for the reaction with that for the M

26 ive intermediate, separated by a significant free energy barrier from the dimer with a native binding

27 au theory of phase transition, the resulting free energy barrier is found to decrease linearly with t

28 two metastable conformations separated by a free energy barrier that is lowered upon omission of fou

29 The low free energy barrier to partial dehydration in the absenc

30 at the expenses of a large increment on the free energy barrier.

31 nding to a diffusive escape process across a free energy barrier.

32 of the free energy of the stalk, whereas the free-energy barrier changes only slightly.

33 e-water interface leads to a lowering of the free-energy barrier for unfolding, resulting in rapid un

34 roton-electron transfer mechanism that has a free-energy barrier of 6.65 kcal.mol(-1).

35 xplain how the hydrazide catalyst lowers the free-energy barrier of the Cope rearrangement via an ass

36 pose that this structure defines the highest free-energy barrier of the overall catalytic cycle and h

37 lity-dependent shifts in the location of the free-energy barrier to folding.

38 ctuation that kicks the system over a single free-energy barrier.

39 hly polar transition state, leading to lower free energy barriers and higher dipole moments.

40 The reaction free energies and free energy barriers are found to be significantly influ

41 ple crystal phases that interconvert without free-energy barriers and could provide approaches to con

42 iffusion is due to an abrupt decrease in the free-energy barriers for lateral mobility of outer-spher

43 llow the estimation of the bond dissociation free energies BDFE(MH) of the unoxidized hydrides MHL(n)

44 have an exceptionally low bond dissociation free energy (BDFE(C-H) ~ 29 kcal mol(-1) and 25 kcal mol

45 n alkoxy radical utilizing bond-dissociation free energy (BDFE) as the thermodynamic driving force.

46 tential and pK(a), the O-H bond dissociation free energy (BDFE) of hydroperoxide species HP was calcu

47 ature as quantified by the bond dissociation free energy (BDFE), yet only a handful of copper-bound O

48 alculate the corresponding bond dissociation free energies (BDFEs) of stable PCET reagents in nonaque

49 to the single-stranded toehold provides the free energy bias of the reaction.

50 le to the changes in gramicidin dimerization free energy by drug-induced perturbations of lipid bilay

51 alignment, probability analysis, and binding free energy calculation, we predict that a few residues

52 nation with hybrid quantum/classical (QM/MM) free energy calculations to explore how proton pumping r

53 We demonstrate the power of CSP methods and free energy calculations to rationalize the observed elu

54 based on molecular dynamics simulations and free energy calculations with nonequilibrium approaches;

55 and structures here reported were driven by free energy calculations, and provide new insights on an

56 Binding free energy calculations, hydrogen bond analysis, per-re

57 rella sampling simulations are performed for free energy calculations, revealing a higher energy barr

58 d experimentally, in good agreement with our free energy calculations.

59 mechanics molecular dynamics simulations and free energy calculations.

60 Second, our free-energy calculations reveal that the affinity of the

61 An additional 14 mus of free-energy calculations shows that the energy necessary

62 rounds of optimization used relative binding free-energy calculations to prioritize different substit

63 ons are linked to an increased overall Gibbs free energy change (DeltaG(Overall)) and a potential bio

64 We addressed this question by measuring the free energy change for a number of backbone hydrogen bon

65 As cellular inputs, ketones increase Gibbs free energy change for ATP by 27% compared to glucose.

66 and DeltaG degrees (d) , to find the overall free energy change from the two neutral species to compl

67 conductive oxide as a function of the Gibbs free energy change.

68 the chemisorption of nitrogen and the lower free-energy change for the *NNH formation, and the 3D al

69 The calculated free energy changes (DeltaDeltaG(asc)) caused by mutatio

70 The magnitudes of the backbone hydrogen bond free energy changes in our study are comparable to those

71 Additionally, the free energy changes observed upon cysteine incorporation

72 model to quantitatively evaluate the binding free energy changes of SARS-CoV-2 spike glycoprotein (S

73 tein-angiotensin-converting enzyme 2 binding free energy changes.

74 ciples-such as the optimal way to distribute free-energy changes and barriers across the machine cycl

75 ructure lead to substantial contributions to free energies, consequential enough that they must be co

76 ty generally increases as the conformational free energy contribution from one or more sites is stren

77 odel that allows for variable conformational free energy contributions from distinct sites, and assoc

78 eta- and gamma-herpesvirus NECs, the binding free energy contributions of residues displayed from ide

79 A free-energy correlation demonstrates that the percent in

80 We first determine the conformational free-energy cost of the substrate expansion due to the b

81 simulation methodology, we estimate that the free-energy cost of this membrane perturbation is in the

82 ased on the N-H bonds of ammonia in a carbon-free energy cycle.

83 ondary structure prediction programs utilize free energy (DeltaG degrees 37) minimization and rely up

84 t of dissociation since the activation Gibbs free energy (DeltaG(*)) was lower for the former (DeltaG

85 he dominating active centers with the lowest free energy (DeltaG) for CO(2) reduction.

86 g with the environment modifies the reaction free energy, DeltaG(gamma), and the reorganization energ

87 se interactions can significantly affect the free energy, DeltaG, of marginally stable and low-popula

88 e and its protein substrates but also by the free energy difference between the conformational ensemb

89 forms a theoretical basis in recovering the free energy difference between two states from exponenti

90 As a result, the free energy difference for the formation of *COOH is low

91 rom the crystal and determine from these the free-energy difference between the phases and the interf

92 y decreases with increasing cation hydration free energy, except for lithium.

93 (IMS) and mass spectrometry (MS) to map the free energy folding landscape.

94 The free energies for fibril formation were -12.36, -8.10, a

95 that catalyze ATP-hydrolysis and utilize its free energy for a staggering range of functions from tra

96 ar electron transfer in MHCF optimizes Gibbs free energy for hydrogen adsorption (DeltaG(H*) ) near z

97 ctanoyl-CoA binding increases the activation free energy for the unfolding reaction of ACBP without a

98 We find the effective Ginzburg-Landau free energy for this model and determine the spectrum of

99 ng steps, diffusion coefficients and binding free energies from potential of mean force estimations w

100 This requires inferring free energies from the equilibrium simulations, and extr

101 Electron bifurcation uses free energy from exergonic redox reactions to power ende

102 NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone

103 ed here in the context of a Landau-de Gennes free energy functional.

104 The free energy gap between the ground (RC) and the [Formula

105 culations were used to compute the T(1)-S(0) free energy gap of the olefin-tethered precursors and al

106 hes of machines and organic life promise new free-energy-governed selection of intelligent digital li

107 ta), involve transitions from the disordered free energy ground state to assembly-competent states.

108 deeply inserted tryptophans that have lower free energy in the LD oil phase and positively charged r

109 ces, the CB interface has the least area and free energy, in both capsids.

110 substituent contributions to ligand-binding free energies is challenging due to nonadditive effects.

111 ction, but in this case none of the released free energy is conserved.

112 How much free energy is irreversibly lost during a thermodynamic

113 The free energy is partitioned into three parts: 1) the inne

114 Available Gibbs free energy is reduced by 71 to 86% across the habitable

115 c transformation demonstrates that the Gibbs free energy is the driving force for the transformation.

116 and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the tran

117 he crystallization kinetics proceed down the free energy landscape in a multistage process where each

118 ers take over the unfolding and dissociation free energy landscape in a vacuum.

119 e of how to chemically access the underlying free energy landscape in MOFs.

120 e model, no matter how rugged its underlying free energy landscape is: In other words, this distribut

121 h by computing via molecular simulations the free energy landscape of DNA origami hinges actuated bet

122 ecular dynamics simulations to determine the free energy landscape of E7.

123 n enthalpies and entropies that comprise the free energy landscape of transfer hydrogenation catalysi

124 Using the free energy landscape we propose the pathway of Abeta25-

125 o estimate the barriers on the corresponding free energy landscape.

126 the reaction rates defined by an underlying free energy landscape.

127 ure control the reaction pathway through the free energy landscape.

128 We report the free-energy landscape and thermodynamics of the protein-

129 By computing the conformational free-energy landscape associated with the activation of

130 e the resulting structures to the underlying free-energy landscape by combining in-situ atomic force

131 The current work demonstrates how the free-energy landscape determines the behaviour of differ

132 ed static snapshots fail to represent a full free-energy landscape due to homogenization in structura

133 We predict that a simple and universal free-energy landscape enables electron bifurcation, and

134 Calculating the free-energy landscape for distinct tRNA species implicat

135 ynamics to reconstruct the tension-dependent free-energy landscape for the opening transition in MscL

136 measure cruciality by changes in the capsid free-energy landscape partition function when an interac

137 phase transition, we construct an effective free-energy landscape that describes the formation jitte

138 In addition to predicting a free-energy landscape that is consistent with previous e

139 d-in-hand, allowing the protein to adapt its free-energy landscape to incoming signals.

140 Given this forbidding free-energy landscape, mechanisms have evolved that cont

141 e rationalized by a remodeling of its rugged free-energy landscape, with very subtle shifts in the po

142 The conformational free energy landscapes of free alpha-l-arabinofuranose a

143 driver mutations, release of autoinhibition, free energy landscapes, and targeted pharmacology in pre

144 de critical, detailed information on folding free energy landscapes, intermediates, and pathways.

145 or and the G(i) to calculate two-dimensional free energy landscapes.

146 ydrophilic zeolite catalysts modify reaction free energy landscapes.

147 of changing concentration on the aggregation free-energy landscapes and to predict the effects of pho

148 ons of advanced methods for sampling complex free-energy landscapes at near nonergodicity conditions

149 We also use enhanced sampling to compute the free-energy landscapes corresponding to our experiments

150 The underpinning free-energy landscapes for electron bifurcation were als

151 Analogous to free-energy landscapes for multipathway protein folding

152 The model predicts free-energy landscapes for the different RNA hairpin-for

153 reaction coordinates were used to calculate free-energy landscapes that capture the full process and

154 are easily described by order parameters and free-energy landscapes, for their non-stationary counter

155 been a shift away from the classical minimum free energy methods to partition function-based methods

156 molecular dynamics simulations combined with free-energy methods.

157 slowness is even more severe than cubic-time free energy minimization due to a substantially larger c

158 stent with our computer simulations based on free energy minimization.

159 cial (EEI) model, based on quasi-equilibrium free-energy minimization of disordered, screened-charge-

160 rganism-centered concept of fitness based on free-energy minimization, toward a social system-centere

161 the overhangs collectively introduce a sharp free-energy minimum at the closed state and a broad ener

162 during association process which is a local free-energy minimum having ~50-60% of native contacts.

163 esign of stable proteins with a single, deep free-energy minimum, the design of conformational switch

164 ns on the electronic structures and relative free energies of 5-exo and 6-endo cyclization pathways s

165 lexes have comparable Rh-H bond dissociation free energies of 51.8 kcal mol(-1) for (eta(5)-C(5)Me(5)

166 Here, we computed relative binding free energies of a prototypical Hv1 blocker on a model o

167 echanism, which has intrinsically high 298 K free energies of activation (in excess of 30 kcal mol(-1

168 ecular dynamics (MD) simulations, activation free energies of chemical steps were calculated using de

169 ain accurate structural and absolute binding free energies of Co(2+) and Ni(2+) to the enzyme glyoxal

170 ch are discussed, and we note that predicted free energies of fourteen out of the sixteen cases agree

171 alize the effect of functionalization on the free energies of nitrone reactivity with hydroxymethyl r

172 PFASs and hPXR, showing how relative binding free energies of PFASs relate to hPXR agonism.

173 By comparing the free energies of the reactants and transition states for

174 ence of a single binding site with a binding free energy of -24 kJ/mol.

175 und II) and a free NO(2) radical via a small free energy of activation.

176 the surface equilibrium constant, the Gibbs free energy of adsorption, and the surface coverage were

177 anic phosphate, adenosine diphosphate, Gibbs free energy of ATP hydrolysis (DeltaGATP), phosphomonoes

178 ochemical gradients, so the protein uses the free energy of ATP hydrolysis to transport them.

179 Entropic contributions to the free energy of binding are particularly difficult to ass

180 free-energy relationship with respect to the free energy of binding in the host-guest complex.

181 meric ligand-gated ion channel, converts the free energy of binding of the neurotransmitter acetylcho

182 of host reorganization contributions in the free energy of binding.

183 ects the binding rate and torque affects the free energy of bound stator units captures the observed

184 operties such as enthalpy, entropy and Gibbs free energy of dissolution were obtained using experimen

185 demonstrate how the experimentally measured free energy of each step directly contributes to the <50

186 ough its intra-dimer interface has the least free energy of formation.

187 cal calculations elucidate that the reaction free energy of HCOO* protonation is decreased on the V(O

188 sesses a thermal neutral and desirable Gibbs free energy of hydrogen for HER, ascribed to the tailori

189 provide useful mechanistic insights into the free energy of interaction between the monomers as well

190 insights into the monomer exchange rates and free energy of interactions between the monomers that di

191 , but can only be achieved if the changes in free energy of intermediate steps are minimized and the

192 differing composition and are powered by the free energy of mixing.

193 PR and electrochemical data, we quantify the free energy of Pd dimerization as <-4.5 kcal/mol for Pd(

194 electivity, and since KED is affected by the free energy of reaction and asynchronicity (factor eta)

195 The Gibbs free energy of surface adsorption can be accurately eval

196 The free energy of the distribution of CNs is found to be a

197 odel simultaneously reproduces the solvation free energy of the individual TM ions and reproduces the

198 ain an accurate value for the bulk hydration free energy of the Na(+) ion.

199 re we strive to formulate it based on Gibb's free energy of the solid-fluid system and on the recentl

200 such as PE lipids have little effect on the free energy of the stalk barrier, likely because of its

201 ranes is the most crucial determinant of the free energy of the stalk, whereas the free-energy barrie

202 MPfold web server for the calculation of the free energy of TM helix association (DeltaG(asc)) in TM

203 This was also confirmed by quantifying the free energy of translocation for the two drugs via molec

204 vity parameter sigma ~6 x 10(-5) and a Gibbs free energy of unfolding of g(nu) ~100 cal/mol per amino

205 ship between the concentration of FA and the free energy of unfolding with a slope of m (FA+pH) (the

206 es relative to the inactive forms, including free energy, partial molar volume, and compressibility.

207 The minimum free energy path between the CIP and SIP becomes smoothe

208 biochemical analyses to delineate an optimal free energy path connecting the polymerization and exonu

209 The minimum free energy paths for the tautomerization from the wG-T

210 A favorable free energy pathway of late-stage functionalization of (

211 ent a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical sy

212 Recent improvements to the free energy perturbation (FEP) calculations, especially

213 Free energy perturbation (FEP) has been applied to predi

214 ven docking model and including a systematic free energy perturbation (FEP) study.

215 ked morpholines, a modification motivated by free energy perturbation (FEP+) calculations.

216 was analyzed with one of the most exhaustive free energy perturbation studies on a GPCR, obtaining an

217 We used alchemical free energy perturbation techniques based on atomistic m

218 The free-energy perturbation (FEP) calculations were perform

219 Alchemical free-energy perturbation calculations indicate that the

220 s almost completely, but if its partitioning free energy prefers one leaflet over the other, the resu

221 However, we are not convinced that the free energy principle and Thinking Through Other Minds w

222 any self-organising system complies with the free energy principle, in virtue of placing an upper bou

223 Using the free energy principle, which bridges information theory

224 concept of culture to show how TTOM and the free-energy principle (FEP) can capture essential elemen

225 re are serious theoretical problems with the free-energy principle model, which are shown in the curr

226 through other minds creatively situates the free-energy principle within real-life cultural processe

227 esian brain hypothesis, as formalized by the free-energy principle, is ascendant in cognitive science

228 r account of culture and social norms in the free-energy principle, which postulates that the utility

229 lity for (i) an empirical examination of how free-energy principles explain dynamic cultural behavior

230 th the experimentally derived real hydration free energy produces an effective surface potential of w

231 e gas emission while we transition to carbon-free energy production.

232 ation of properties of interest, such as the free energy profile and the mean first passage time.

233 hod and free energy sampling to quantify the free energy profile and timescale of the proton transpor

234 nknotted denatured state to characterize the free energy profile associated to both folding pathways.

235 The free-energy profile also captured the crucial role of al

236 We then characterize the rates and the free-energy profile associated with this heterogeneous n

237 nine rate constants to establish a complete free-energy profile including the rates of DNA transloca

238 Unfolding free energy profiles determined by BXD suggest that the

239 Free energy profiles for Na(+) and for Cl(-) ions within

240 mbrella sampling (US) techniques and provide free energy profiles for unfolding of talin rod subdomai

241 Remarkably, the free energy profiles in gas phase and in CotB2 are surpr

242 The free energy profiles reveal stabilization of partially u

243 uded from the DNA helix and their associated free energy profiles.

244 rella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarb

245 xes were determined using a state-of-the-art free energy protocol and were found to be in good agreem

246 cy between 5.5 and 7.0 and followed a linear free energy relationship (LFER) proposed in a previous s

247 The linear free energy relationship accurately described the data c

248 elical hairpin domain HP2 and applied linear free energy relationship analysis to infer that the tran

249 work, we studied how carbonate affected the free energy relationship by examining the effect that ca

250 ic driving force of the reaction in a linear free energy relationship that was a function of the solu

251 magnitude and can be expressed by the linear free-energy relationship lg K(I) = s(I) LA(I) + LB(I), w

252 on, precision nucleobase mutation and linear free-energy relationship measurements with molecular dyn

253 ding nuclei, as probed by analysis of linear free-energy relationship plots.

254 polarity parameter, E(T)(30), shows a linear free-energy relationship with respect to the free energy

255 salicylaldehydes and TRIS in a set of linear free energy relationships (LFER), we disclose how the fo

256 local parametrization approaches and linear free energy relationships (LFERs) along with multivariat

257 Here we demonstrate that linear free energy relationships (LFERs)-including Hammett and

258 ium concentrations, and polyparameter linear free energy relationships (pp-LFERs) for aqueous adsorpt

259 The linear free energy relationships between rate constants and pK(

260 By using hydricity, quantitative linear free energy relationships can be developed to relate the

261 Polyparameter linear free energy relationships coupled with a composition-bas

262 f the computational model on computed linear free-energy relationships (LFER) and the nature of the t

263 phase transition incurs the smallest loss of free energy relative to its predecessor.

264 ort of a galactoside with an H(+), using the free energy released from downhill translocation of H(+)

265 A significant part of the free energy released in this exergonic process is conser

266 rea (a neutral denaturant) alter the folding free energy remains indistinguishable whether proteins a

267 he main active site and reduces the reaction free energies required for CO(2) activation and C-C coup

268 Thermodynamic hydricity represents the free energy required for heterolytic cleavage of the met

269 he interfacial potential contribution to the free energy resides in the long-range term.

270 l and theoretical infrared spectroscopic and free-energy results of this work show the emergence of t

271 scale reactive molecular dynamics method and free energy sampling to quantify the free energy profile

272 With a goal of determining an absolute free energy scale for ion hydration, quasi-chemical theo

273 Surface free energy (SFE) of micro- and nanoparticles plays a cr

274 Free energy simulations rationalized how ThyX recognizes

275 Our free energy simulations reveal that Y731 is able to samp

276 amer sticks into the pore and plugs it, with free energy simulations showing that this is a strong in

277 We combined free energy simulations, biochemical assays and evolutio

278 employed molecular dynamics simulations and free energy simulations.

279 ntum mechanical/molecular mechanical (QM/MM) free energy simulations.

280 itio quantum mechanical/molecular mechanical free-energy simulations to gain insight into the catalys

281 ded molecular dynamics and enhanced sampling free-energy simulations, we observed that the carboxyl s

282 The landscape relies on steep free-energy slopes in the two redox branches to insulate

283 s to use N-based fuels as alternative carbon-free energy sources.

284 ationalized from the sparsely populated high free energy states of the monomers?

285 orithm that predicts the approximate minimum free energy structure in linear time, we design a simila

286 the molecular details, we first compute the free-energy surface (FES) of insulin dimer dissociation

287 st the applied torque are reflections of the free-energy surface of the systems.

288 mutation-induced perturbation of the folding free-energy surface that increases the populations of hi

289 Sampling complex free-energy surfaces is one of the main challenges of mo

290 s thermally stable, having bond dissociation free energies that are over 50 kJ/mol below those of the

291 on between two different crystal phases with free energies that depend on the crystal size.

292 t can be used to determine the thermodynamic free energies that underlie LLPS.

293 f the ion with nearby waters, 2) the packing free energy that is the work to produce a cavity of size

294 In various systems, ranging from solvation free energies to protein conformational transition rates

295 ew central questions in their performance as free energy transducers, outline theoretical and modelin

296 ibe hydrophobicity in terms of the hydration free energy using grid inhomogeneous solvation theory (G

297 ize the role of mutations, we calculated the free energy variation upon mutations in the available pr

298 ollowing the order dictated by their binding free energies with no intermediate states.

299 d is able to detect small changes in binding free energy with a sensitivity comparable to in vitro me

300 Hence, we consider a balance of curvature free energy with hydrophobic matching and demonstrate ho