ライフサイエンスコーパス: atomistic

1 ssue by computationally modeling a plausible atomistic 3D structure of ApoE4.

2 Here we used atomistic accelerated molecular dynamics (aMD) simulatio

3 , our study highlights the importance of the atomistic and chemical nature of the tunneling medium at

4 We performed comparative atomistic and coarse-grain molecular-dynamics simulation

5 esign, and the complementary roles that both atomistic and coarse-grained approaches play in such sim

6 molecular-dynamics simulations with combined atomistic and coarse-grained description of NPs reveal t

7 Here the authors show atomistic and coarse-grained modelling combined with enh

8 a multiscale simulation approach that blends atomistic and coarse-grained models.

9 Here, we use atomistic and coarse-grained molecular dynamics simulati

10 ch less computationally demanding than fully atomistic and coarse-grained simulation methodologies; h

11 egrated computational strategy that combined atomistic and coarse-grained simulations with coevolutio

12 On the basis of this atomistic and electronic structure information, we propo

13 odels for the environment through the use of atomistic and polarizable embeddings.

14 The LJ potential models atomistic attraction and repulsion with century old pres

15 iscovery of these lattices 45 years ago, the atomistics behind the ordering mechanisms responsible fo

16 We performed a set of atomistic biased MD simulations running a total of 15.6

17 Here we present the first semi-quantitative atomistic calculation of the formation of edge dislocati

18 Using pseudopotential atomistic calculation on a model type-II semiconductor h

19 ermal transport behaviour, corroborating our atomistic calculations in unveiling the role of molecula

20 Electronic structure and atomistic calculations point to the interplay between th

21 tegy using phylogenetic analysis and Rosetta atomistic calculations to design PfRH5 variants with imp

22 dant hydrogenated vacancies, verified by our atomistic calculations.

23 ed by demonstrating the capability to retain atomistic characteristics of the wave propagation behavi

24 (TEM) and Raman spectroscopy, but a dynamic, atomistic characterization has remained elusive.

25 Atomistic classical molecular dynamics simulations furth

26 Here we show atomistic, coarse-grained modelling combined with advanc

27 Here, we use a multistage atomistic-coarse-grained approach, complemented by circu

28 Using atomistic computer simulation to predict this residence

29 depth distribution of defect clusters and an atomistic computer simulation.

30 ve exceedingly small time and length scales, atomistic computer simulations can provide unique insigh

31 evidence on the influence of the Al-induced atomistic configurational change on the mechanical prope

32 mpling technique to calculate well-converged atomistic conformational ensembles of the intrinsically

33 imental challenge for this field is exerting atomistic control over the structure and composition of

34 Here, using in situ HRTEM, we captured the atomistic conversion reaction processes during Li, Na, C

35 To address this question, we used a fully atomistic CTF model to test both Ca(2+) binding strength

36 A full atomistic description of the different reaction products

37 Here we show in atomistic detail how the human beta2-adrenergic receptor

38 Finally, the direct retrieval of fully atomistic detail is possible through backmapping, openin

39 e binding to a prototypical iGluR, GluA2, in atomistic detail using unbiased molecular simulations.

40 res that determine Fe(2+) translocation with atomistic detail, and we propose a putative mechanism fo

41 e states and the dynamics of backtracking at atomistic detail.

42 sms that are progressively being revealed in atomistic detail.

43 es that are still too large to be studied in atomistic detail.

44 final stage of the translocation process in atomistic detail.

45 Little is known of the atomistic details about how Ryd binds to RyRs.

46 s is critical for the switching process, its atomistic details are not well understood.

47 r applicability with respect to defining the atomistic details of membrane-binding proteins.

48 ological processes which range in scale from atomistic details to an entire metabolic network.

49 lar dynamics (MD) simulation in the range of atomistic displacements and rationalized with a simple m

50 dentified over the years, but the underlying atomistic dynamics have remained difficult to observe.

51 e usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive

52 nger be applicable and quantum plasmonic and atomistic effects could become relevant.

53 Here we introduce an atomistic electrodynamics model where the traditional de

54 sics behind such a mechanism by studying the atomistic electronic structure of the magnetic quasipart

55 ess that has been achieved to understand the atomistic energetics and dynamics of ion-molecule reacti

56 Atomistic, equilibrium simulations at two salt concentra

57 mus of simulation trajectories, we obtained atomistic evidence for the nonselective nature of TRPV1.

58 hous shear bands in B6O, provide a plausible atomistic explanation for the influence of nanotwins on

59 Here we develop an atomistic framework based on microscopic Maxwell's equat

60 In recent years, atomistic free energy calculations have proven to be a v

61 Using an atomistic graph with energy-weighted covalent and weak b

62 disparity remains unknown due to the lack of atomistic information on the catalase-like reaction in H

63 These results provide critical atomistic insight into the aggregation pathway of Abeta4

64 the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DN

65 This study reveals a high- resolution atomistic insight of the [GeTe/Sb2Te3] interfacial struc

66 Structures of protein complexes provide atomistic insights into protein interactions.

67 to date, the sublimation, self-assembly and atomistic insights of expanded porphyrins on surfaces ha

68 ural dynamics, here we developed a series of atomistic integrative models with available crystal stru

69 The simulations provide atomistic interpretations of the peptide-H(+) + surface

70 Using atomistic Landau-Lifshitz-Gilbert simulations we quantif

71 Friction in ordered atomistic layers plays a central role in various nanosca

72 vacancies can be captured quantitatively at atomistic level by mapping the vacancy formation energie

73 Here we use atomistic level modeling and well-tempered metadynamics

74 nd representative examples describing at the atomistic level of detail the structural modalities and

75 , but the nature of carrier transport at the atomistic level remains elusive.

76 uring the kinetic steps of permeation at the atomistic level with a dynamic mechanistic model describ

77 omplex dynamic changes in the catalyst on an atomistic level, highlighting a new way to tailor struct

78 nel family is currently not understood at an atomistic level.

79 ynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level.

80 ,4-benzothiazin-3(4H)-one) inhibition at the atomistic level.

81 ligomerization into the final pore assembly, atomistic-level detail of the protein-lipid interactions

82 ne under ultrafast MAS conditions to provide atomistic-level elucidation of the complex heterogeneous

83 Atomistic magnetic modelling of nanoparticles with and w

84 the best of our knowledge, this is the first atomistic MD simulation that samples the free energy sur

85 Here we present atomistic MD simulations of the monomeric N-glycosylated

86 We use atomistic MD simulations to reveal the details of covale

87 Atomistic mechanics modeling further reveals the depende

88 pre-steady-state kinetics reveals a detailed atomistic mechanism for selectivity of the successful ca

89 tructural transformations provide a detailed atomistic mechanism for the activation process in GPCR,

90 These data led us to propose an atomistic mechanism in which the oxygen radical initiate

91 eriodic boundary conditions to determine the atomistic mechanism underlying catalytic activation of p

92 se quantum mechanics to predict the detailed atomistic mechanisms responsible for C1 and C2 products

93 We predict the atomistic mechanisms underlying electrochemical reductio

94 rganic compounds is important, and providing atomistic mechanistic insights about the reaction mechan

95 mental timescales using a metadynamics-based atomistic method.

96 ed chassis with a design process that avoids atomistic mimicry of natural proteins.

97 anges across the transition and formulate an atomistic minimum energy transition path to explain its

98 ) rapidly computes a SAXS profile of a given atomistic model and fits it to an experimental profile.

99 l x-ray scattering experiments to produce an atomistic model for phosphatidylserine recognition by th

100 l measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor

101 s and solid-state NMR was used to present an atomistic model of a polypyridylruthenium(II) complex bo

102 Here, we report an atomistic model of the excited state ensemble of a stabi

103 Along with a fully atomistic model of the outward-facing conformation in me

104 We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM

105 present a fast and reliable hybrid continuum-atomistic model that couples the protein to the membrane

106 mer-DNA complex was performed by means of an atomistic model that included the tetramerization helice

107 An atomistic model, supported by atomic force microscopy me

108 ids is critical for device applications, and atomistic modeling methods have been developed for bulk

109 imulation approach, combining minimalist and atomistic models (SOP-AT).

110 The method relies on atomistic models and a polarizable force field to descri

111 Comparison of atomistic models of a native cyanobacterial form (Thermo

112 The data enabled generating atomistic models of CRF- and CRF(12-41)-bound CRF1R, fur

113 ling method for constructing high-resolution atomistic models of nucleosomes based on HRF experiments

114 We have constructed the first atomistic models of the Bax oligomeric pore consisting w

115 for CaM with and without binding targets in atomistic models using Jarzynski's equality.

116 simulations based on both coarse-grained and atomistic models with coevolutionary sequence analysis t

117 erone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analys

118 Unfortunately, atomistic molecular dynamics (MD) simulations cannot dir

119 ographic structure of the complete receptor, atomistic molecular dynamics (MD) simulations have recen

120 Atomistic molecular dynamics (MD) simulations of protein

121 In this work we present atomistic molecular dynamics (MD) simulations that sampl

122 Our models combine atomistic molecular dynamics (MD) with coarse-grained si

123 Analysis of >50-mus atomistic molecular dynamics and enhanced sampling traje

124 imulate CypA using multiple-microsecond-long atomistic molecular dynamics in explicit solvent and car

125 d by a combination of continuum analysis and atomistic molecular dynamics simulation.

126 By combining atomistic molecular dynamics simulations and oocyte perm

127 Here, atomistic molecular dynamics simulations are used to exa

128 Based on extensive (7.5 mus total) atomistic molecular dynamics simulations here we show th

129 We report the results of atomistic molecular dynamics simulations informed by qua

130 Through atomistic molecular dynamics simulations of a series of

131 Atomistic molecular dynamics simulations of an assembly

132 Based on atomistic molecular dynamics simulations of cytochrome c

133 Here we combine multimicrosecond atomistic molecular dynamics simulations of dinucleosome

134 the Protein Data Bank structure analysis and atomistic molecular dynamics simulations of glycosylated

135 detergent destabilization of GPCRs, we used atomistic molecular dynamics simulations of thermostabil

136 Atomistic molecular dynamics simulations of wild type an

137 ave studied H-channel function by performing atomistic molecular dynamics simulations on the entire,

138 , vibrational sum frequency spectroscopy and atomistic molecular dynamics simulations reveal how Ca(2

139 Fully atomistic molecular dynamics simulations show that the f

140 Atomistic molecular dynamics simulations support a mecha

141 Here, we report the results of atomistic molecular dynamics simulations that elucidated

142 We used quantitative spatial imaging and atomistic molecular dynamics simulations to examine mole

143 In this work, we use atomistic molecular dynamics simulations to investigate

144 s, photobleaching/activation approaches, and atomistic molecular dynamics simulations to uncover the

145 Atomistic molecular dynamics simulations were performed

146 By comparing the results of atomistic molecular dynamics simulations with experiment

147 ity measurements, accompanied by large-scale atomistic molecular dynamics simulations, are used for t

148 Based on atomistic molecular dynamics simulations, we propose a m

149 tural properties of these assemblies through atomistic molecular dynamics simulations.

150 an be easily implemented in any software for atomistic molecular dynamics simulations.

151 a combination of spectroscopic methods with atomistic molecular dynamics simulations.

152 bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations.

153 gadalton pointer structure by means of fully atomistic molecular dynamics simulations.

154 reproduce the distortions observed in fully atomistic molecular dynamics simulations.

155 Here, we present atomistic molecular dynamics studies of the closed-state

156 ant information we performed a comprehensive atomistic molecular dynamics study which revealed that i

157 In the present study we have utilized atomistic molecular dynamics to perform umbrella-samplin

158 Recently, a pseudo atomistic molecular model has emerged as a valuable tool

159 RASSF5, and MST2 SARAH domains by using both atomistic molecular simulation techniques and experiment

160 Atomistic molecular simulations indicate that the stabil

161 mbrane interactions of Abeta42, we performed atomistic molecular-dynamics (MD) simulations to charact

162 olecular structure that we address here with atomistic molecular-dynamics simulations remains controv

163 Here, we use atomistic molecular-dynamics simulations, coarse-grained

164 The model employs an atomistic (molecular dynamics) representation of a fract

165 olve several long-standing puzzles about the atomistic OER mechanism.

166 Theoretical calculations reveal their atomistic origin as the local reconstruction of domain w

167 the presence of a copper tip and reveal the atomistic origin of the process.

168 ical concept in fundamental understanding of atomistic pathways in topological interface transitions

169 This study provides a full atomistic picture of the transition from intercalation t

170 e to determine separately the orientation of atomistic planes defined through the naphthalenediimide

171 trategies, it is essential to understand the atomistic processes that lead to bubble formation and su

172 re provide a basis with which to explore the atomistic properties and hence mechanisms involved in Ti

173 Full-band atomistic quantum transport simulations establish phosph

174 Full-band atomistic quantum transport simulations of phosphorene n

175 constant potentials to examine the detailed atomistic reaction mechanism of OER at the IrO2 (110) su

176 of CO2 to hydrocarbons and alcohols, but the atomistic reaction mechanism that controls the product d

177 emperatures high-strain compression promotes atomistic rearrangements in Al0.1CrCoFeNi, resulting in

178 Atomistic reconstruction of signaling pathways in the Dn

179 or this purpose, we have performed extensive atomistic Replica Exchange Molecular Dynamics simulation

180 Within atomistic replica-exchange molecular dynamics (REMD), we

181 Here, we have performed extensive atomistic replica-exchange molecular dynamics simulation

182 e for the first time accurately evaluated at atomistic resolution comparing absolute binding free-ene

183 ding of these molecular binding processes at atomistic resolution requires formally the complete desc

184 namics in organic conjugated dendrimers with atomistic resolution, a phenomenon expected to universal

185 uman protein disulfide isomerase (hPDI) with atomistic resolution.

186 ein are investigated for the first time with atomistic resolution.

187 d stable isotope labeling scheme, to measure atomistic-resolution transmembrane-transmembrane interac

188 ural changes on the mechanical properties at atomistic scale is not well understood.

189 In 50 mm NaCl buffer, atomistic scattering modeling showed that both C3b and C

190 , we report the development of a large-scale atomistic scheme providing a microscopic insight into th

191 the significant role of GB character in the atomistic SCM process and contribute to the future desig

192 od to jointly exploit the power of ab initio atomistic simulation along with the information carried

193 Here we first apply atomistic simulation techniques and quantum/statistical

194 h have not previously been characterized via atomistic simulation techniques.

195 We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from

196 However, atomistic simulations accurately capture every possible

197 ers a way to characterize the wear volume in atomistic simulations and atomic force microscope wear e

198 Here, using classical atomistic simulations and density functional theory calc

199 their effective interactions, obtained from atomistic simulations and experiments, into a statistica

200 ransmission electron microscope, large-scale atomistic simulations and finite element modelling show

201 Here, we conduct both atomistic simulations and theoretical modeling to show t

202 Here, through both atomistic simulations and variable-strain-amplitude cycl

203 dy of ion irradiation, ion beam analysis and atomistic simulations are carried out on a unique set of

204 Here, experiments and atomistic simulations are synergically used to elucidate

205 Atomistic simulations are well positioned to answer open

206 Our microsecond-long atomistic simulations elucidate key structural differenc

207 Atomistic simulations elucidate the overall mechanism an

208 nt study clearly demonstrates the promise of atomistic simulations for detailed characterization of I

209 A series of mixed quantum-classical atomistic simulations illustrate that dielectric induced

210 1/2<110>{100} edge dislocation by performing atomistic simulations in 4-12% doped CeO2 as a model fas

211 Here, atomistic simulations in Mg reveal the unusual mechanism

212 Given the well-known limitations of atomistic simulations in sampling biomolecular systems,

213 s, a combination of theoretical modeling and atomistic simulations indicates that the formation of si

214 Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-Tyr(B26)]insulin to pre

215 d with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as p

216 Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity

217 perimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemb

218 We present fully atomistic simulations of cold denaturation of an alpha-h

219 For example, it has been proposed using atomistic simulations of crack propagation in elastic ma

220 dy the crystallization of amorphous Ge using atomistic simulations of critical nano-metric nuclei at

221 Herein, we leverage atomistic simulations of graphite to extend the ripploca

222 One of the major challenges in atomistic simulations of proteins is efficient sampling

223 We report on atomistic simulations of tantalum that make detailed pre

224 e model is in excellent agreement with fully atomistic simulations of the ion channel gramicidin embe

225 alues agree well with direct observations or atomistic simulations of the same quantities, suggesting

226 In particular, atomistic simulations of ubiquitin in solution based on

227 Both the theoretical modeling and atomistic simulations predict that the adhesion induced

228 Our first-principles-based atomistic simulations provide detailed microscopic insig

229 Additionally, atomistic simulations provide molecular insight into how

230 In situ studies and atomistic simulations reveal that such remarkable self-h

231 X-ray structure of the apo CNBD and atomistic simulations reveal that the isomerization invo

232 Extensive atomistic simulations show that cholesterol regulates be

233 Atomistic simulations show that unidirectional growth is

234 Here we make predictions based on atomistic simulations that form the basis for a new appr

235 e of minutes and thus hard to reproduce with atomistic simulations that have been able to reproduce f

236 These results were coupled with atomistic simulations to better reveal the underlying pr

237 ntegrate high pressure X-ray diffraction and atomistic simulations to correlate the anisotropic defor

238 ated on this hypothesis, we have carried out atomistic simulations to investigate peptide-membrane in

239 In this work we use atomistic simulations to provide detailed thermodynamic

240 e force measurements with coarse-grained and atomistic simulations to resolve the mechanistic basis f

241 this study is the first direct comparison of atomistic simulations to the continuum theories to predi

242 employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p

243 Concurrently, atomistic simulations using binary collision approximati

244 inding site of a GABAA-R homology model, and atomistic simulations were carried out to observe the be

245 Large-scale atomistic simulations were performed in explicit solvent

246 By integrating atomistic simulations with a novel multiscale numerical

247 Using atomistic simulations with model interatomic potentials,

248 by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics.

249 m laboratory directed evolution (LDE), using atomistic simulations with the AMOEBA polarizable force

250 internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analyti

251 uations that agree very well with results of atomistic simulations, even many SDs from the mean and e

252 Our results, integrated with atomistic simulations, negate the hypothesis of a sharp,

253 It allows us to obtain the parameters from atomistic simulations, providing thus a direct connectio

254 , macroscopic information from stochastic or atomistic simulations, such as molecular dynamics (MD).

255 Using atomistic simulations, we calculate the effect of SAM an

256 olution transmission electron microscopy and atomistic simulations, we characterize the dark side of

257 Using ab initio atomistic simulations, we explain this surprising coexis

258 Here, using atomistic simulations, we reproduce the experimental obs

259 olution transmission electron microscopy and atomistic simulations, we show that twinning is the domi

260 In this work, by using large-scale atomistic simulations, we uncover how a 100{011} edge di

261 nsile strength and work of separation, using atomistic simulations.

262 rodimers and analysis of interactions in the atomistic simulations.

263 mutagenesis experiments as well as detailed atomistic simulations.

264 0] group symmetrical tilt GBs in bcc W using atomistic simulations.

265 ent with reported macroscopic values and our atomistic simulations.

266 The microscopic mechanism was unveiled in atomistic simulations.

267 mputed using the output of microseconds-long atomistic simulations.

268 this membrane transport protein, followed by atomistic simulations.

269 ectroscopy and interpreted through ab initio atomistic simulations.

270 nter-diffusion is revealed, and supported by atomistic simulations.

271 antitative and validated through a series of atomistic simulations.

272 sm experiments as well as investigated using atomistic simulations.

273 te approach generalized for ferrimagnets and atomistic spin model simulations show that this remarkab

274 s of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations t

275 overlaps between the volumes occupied by the atomistic structure and 3D EM map, rewards overlaps betw

276 gnificant changes in both the morphology and atomistic structure at the interface were observed when

277 s, one typically aligns (match and fits) the atomistic structure model with the 3D EM map.

278 ontinue to be increasing occurrences of both atomistic structure models in the PDB (possibly reconstr

279 sing this question has been the lack of a 3D atomistic structure of ApoE4 to date.

280 In this perspective, unravelling the atomistic structure that originates the improvements in

281 d using (2)H NMR to yield knowledge of their atomistic structures in relation to equilibrium properti

282 a hybrid computational approach to model the atomistic structures of HBV-RT/DNA-RNA/dATP and HBV-RT/D

283 or the best possible structural alignment of atomistic structures with 3D EM.

284 d electron microscopy into consistent, fully atomistic structures.

285 ten not easily deducible from the underlying atomistic system.

286 s result in realistic 3D models of the MnCat atomistic texture, formed by the interconnection of smal

287 Further, we derive phenomenological and atomistic theories that describe such couplings in a gen

288 Using atomistic tight-binding technique and Hartree self-consi

289 of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the phys

290 lectron microscope, we report on the salient atomistic to micro-scale mechanisms underlying the origi

291 hous Ce100-xAlx (x<25) alloys and reveals an atomistic transformation mechanism.

292 Atomistic understanding of crystallization in solids is

293 The atomistic understanding of the dissociation mechanisms f

294 proved simulation methods now provide better atomistic understanding of the protein dynamics and coop

295 This work opens the door to a detailed atomistic understanding of transformation reactions in e

296 n its agreement with experiment, provides an atomistic view of long-range allosteric coupling in a ph

297 ar dynamics (MD) simulations to arrive at an atomistic view of the conformational dynamics of DNA.

298 Our data provide the first atomistic view of the supercharging mechanism.

299 Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock tech

300 ts for theoretical calculations, which yield atomistic views of the structures that are formed when p