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 Atomistic ab initio calculations are conducted to analyz

3 lobal conformational change, and proposed an atomistic allosteric mechanism leading to the discovery

4 Our atomistic analysis unveils the role of envelope anisotro

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

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

7 scuss the understanding recently revealed by atomistic and coarse-grained computer simulations of nan

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

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

10 With atomistic and coarse-grained molecular dynamics simulati

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

12 We review atomistic and coarse-grained simulation studies of amylo

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

14 esult of the simultaneous alteration of both atomistic and electronic structure.

15 and tested in recent years based on a fully atomistic and polarizable classical modeling of water co

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

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

18 , new noise-filtering analysis protocols and atomistic biomolecular simulations reveals weak binding

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

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

21 Our observations of dislocation motion and atomistic calculations unveil the unexpected dominance o

22 Together with atomistic calculations, we show that the structural osci

23 progress in electronic structure methods and atomistic catalyst models employed, which have enabled t

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

25 dels supply fast and accurate predictions of atomistic chemical properties, they do not explicitly ca

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

27 rning the DNA-vWF interaction by integrating atomistic, coarse-grained, and Brownian dynamics simulat

28 This review is a short survey of the atomistic computational investigations of K(+) and Na(+)

29 Large-scale atomistic computer simulations of materials heavily rely

30 his method, as currently applied, fosters an atomistic conceptualization of defensive behaviors, whic

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

32 Atomistic control of the coordination environment of lat

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

34 Here we present a detailed atomistic description for both.

35 orrect reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ~

36 tical way to couple these phenomena with the atomistic description of chemistry.

37 Atomistic description of protein fibril formation has be

38 Our results yield an atomistic description of the mechanism for a simple prot

39 Collectively, our results provide an atomistic description of the permeability of the HIV-1 c

40 o inform the continuum level with the proper atomistic description.

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

42 We present a study of this system in atomistic detail that elucidates the effects of mutation

43 we track each step of the binding process in atomistic detail with molecular dynamics simulations usi

44 low protein surface concentration with near-atomistic detail.

45 Our results provide novel atomistic details about fundamental aspects of biologica

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

47 Our study thus provides atomistic details of early molecular events occurring wi

48 e molecular dynamics simulations capture the atomistic details of the nanoparticles' formation and ev

49 elate the water intrusion mechanism with the atomistic details of the zeolite crystal, such as defect

50 Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-ligh

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

52 We provide an atomistic, dynamic picture of the unbinding process, rep

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

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

55 e normal and Umklapp processes directly from atomistic dynamics.

56 These atomistic electronic properties are extraordinarily usef

57 The application of atomistic electrostatic potential mapping of both sorben

58 h NMR residual dipolar couplings provided an atomistic ensemble model for HIV-1 TAR, and the model ac

59 ined multiscale approach involving classical atomistic equilibrium and nonequilibrium MD simulations

60 Atomistic, equilibrium simulations at two salt concentra

61 Here we report on over 250 mus of fully-atomistic, explicit solvent, temperature replica-exchang

62 (III), Cr(III), Fe(II), Zn(II)-through fully atomistic, extensive quantum mechanical/discrete molecul

63 Direct molecular dynamics simulations using atomistic force fields could provide such insight, but a

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

65 Atomistic frustration analysis provides a route for scre

66 Atomistic imaging and spectroscopy reveal that metal sub

67 Our methods enable the atomistic imaging of Li-ions in this cathode material in

68 Here, we report the folding of atomistic, implicitly solvated protein systems with fold

69 It is at interfacial boundaries where such atomistic information is most relevant.

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

71 here remain enormous uncertainties about the atomistic interactions at the electrode-electrolyte inte

72 onclusions from simulations studies and also atomistic interpretation of the behavior of experimental

73 Nonetheless, the atomistic knowledge of the nature of the active sites re

74 mentally mapped, and we here set out to gain atomistic level insights into how TETS inhibits the huma

75 mechanisms are revealed by simulating at the atomistic level the whole dynamics of the complex throug

76 The atomistic level understanding of iron speciation and the

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

78 r assessing protein structure predictions at atomistic level).

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

80 experimentally image Li-ion diffusion at the atomistic level.

81 stigate actin-tropomyosin interactions at an atomistic level.

82 t K-Ras, with an integrated investigation of atomistic-level changes, local conformational shifts and

83 Our findings provide an atomistic-level explanation for GCase activation and the

84 Atomistic-level modeling typically utilizes stochastic l

85 Thus, we have computationally connected atomistic-level structural information, obtained by cryo

86 The findings elucidate atomistic Li/Na intercalation mechanisms in BP and show

87 estimates to provide an energetic picture of atomistic localization.

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

89 Unbiased atomistic MD simulations with 1.4 mol% PI(4,5)P(2) in a

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

91 There is an atomistic mechanism for the uptake process with Fe(III),

92 tivating vs inhibiting monobodies reveal the atomistic mechanism underlying allosteric modulation.

93 However, the atomistic mechanisms of permeation through defects in th

94 al for lithium-ion batteries, but underlying atomistic mechanisms remain elusive.

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

96 The atomistic mechanisms underlying the flow regimes are int

97 However, the underlying atomistic mechanistic details of the dynamic instability

98 mental timescales using a metadynamics-based atomistic method.

99 Here, we systematically investigate the atomistic migration of Sigma11(113) coherent GBs in gold

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

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

102 membrane-bound protein complex, we report an atomistic model of the PLC and study its conformational

103 (2016) atomistic model of the thin filament displays a paucity

104 mulations on a fully passivated CsPbBr(3) NC atomistic model.

105 g IC50 values, we resort to a combination of atomistic modeling and machine learning.

106 Atomistic modeling and molecular dynamics simulations ba

107 Atomistic modeling for FHR5 generated a library of 250,0

108 ant tetrasubstituted cyclobutane product via atomistic modeling of the CdSe surface and substrates, d

109 As a result, good agreement between the atomistic modeling results and the linear elasticity mod

110 he important role of stress migration in the atomistic modeling study is identified.

111 second harmonic generation measurements, and atomistic modeling, we demonstrate robust room-temperatu

112 ts are well explained through analytical and atomistic modeling.

113 pe that together with outcomes from advanced atomistic modelling provides new insights in the mechani

114 are discussed with respect to the available atomistic modelling results.

115 he creation of >123,000 physically-realistic atomistic models by Monte Carlo simulations for joint X-

116 The creation of physically realistic atomistic models from known high-resolution structures t

117 cs (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM)

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

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

120 h is available online, can generate detailed atomistic models of protein folding mechanisms while she

121 ctional spin label (BSL) to build and refine atomistic models of protein structure.

122 tons in nanobubbles of monolayer WSe(2) with atomistic models to study how strain induces nanoscale c

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

124 nanoscale disorder requires adequately large atomistic models which today are obtained mainly via the

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

126 We explain these findings using atomistic models, and ascribe them to differences in the

127 a series of descriptors are derived from the atomistic models, and these are used to train a Multi-La

128 ude cheaper computational cost than existing atomistic models.

129 In addition, through atomistic modification of the molecular structure, we va

130 solution by small-angle X-ray scattering and atomistic molecular dynamic simulations show that the st

131 Atomistic molecular dynamic simulations show the impact

132 tion of small-angle x-ray scattering (SAXS), atomistic molecular dynamic simulations, single-molecule

133 lies, we combine sub-tomogram averaging with atomistic molecular dynamics (MD) simulations.

134 y, we describe a multiscale model by linking atomistic molecular dynamics (MD), molecular Brownian dy

135 Atomistic molecular dynamics and metadynamics simulation

136 Experimental synthesis and full-atomistic molecular dynamics modeling are combined to sy

137 Our observation serves as a link between the atomistic molecular dynamics simulation and the bulk mec

138 ormational changes during a 10-mus-timescale atomistic molecular dynamics simulation in an explicit m

139 Herein, using data from a 20 mus-long atomistic molecular dynamics simulation of the oncogenic

140 Atomistic molecular dynamics simulation reveals short-ra

141 Using a combined approach of cryo-EM and atomistic molecular dynamics simulation, we present the

142 with a heterogeneous membrane bilayer using atomistic molecular dynamics simulation.

143 In this study, we have performed long-time atomistic molecular dynamics simulations (1 mus for each

144 dimer distributions, we performed extensive atomistic molecular dynamics simulations and fluorescenc

145 Atomistic molecular dynamics simulations and nuclear mag

146 By combining atomistic molecular dynamics simulations and oocyte perm

147 ) spectroscopy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-che

148 As an alternative, atomistic molecular dynamics simulations are now routine

149 Here, atomistic molecular dynamics simulations are used to exa

150 With this in mind, here atomistic molecular dynamics simulations are used to scr

151 Small angle X-ray scattering combined with atomistic molecular dynamics simulations demonstrate the

152 Atomistic molecular dynamics simulations indicate this i

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

154 Through atomistic molecular dynamics simulations of a series of

155 From analyses of atomistic molecular dynamics simulations of Ca(2+)-bound

156 etadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1

157 rk combining equilibrium and non-equilibrium atomistic molecular dynamics simulations of Na+ binding

158 Atomistic molecular dynamics simulations of P2 on model

159 Atomistic molecular dynamics simulations of wild type an

160 Large-scale atomistic molecular dynamics simulations reveal that ste

161 Microsecond-scale atomistic molecular dynamics simulations showed that 4F

162 Atomistic molecular dynamics simulations starting from S

163 Atomistic molecular dynamics simulations support a mecha

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

165 Here, we use over 25 mus of unbiased atomistic molecular dynamics simulations to identify cho

166 lculations and quantum/classical models with atomistic molecular dynamics simulations to probe the en

167 In this study, we use fully atomistic molecular dynamics simulations to scrutinize t

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

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

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

171 observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a mi

172 ic light scattering, confocal microscopy and atomistic molecular dynamics simulations.

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

174 free energy perturbation techniques based on atomistic molecular dynamics simulations.

175 e-bound K-Ras4B in 1.45-ms aggregate time of atomistic molecular dynamics simulations.

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

177 The model links atomistic molecular simulations of protein-protein inter

178 Fully atomistic molecular-dynamics (MD) simulations of perfluo

179 sheath using elastic constants inferred from atomistic molecular-dynamics (MD) simulations.

180 insulin dimerization and dissociation using atomistic molecular-dynamics simulation in explicit wate

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

182 l membrane is consistent with time-resolved, atomistic, molecular dynamics (MD) simulations of phosph

183 n macroscopic thermodynamics, neglecting the atomistic nature of the liquid-solid interface.

184 The atomistic nature of the output extended our understandin

185 Being able to identify the atomistic nature of these sites and the first steps of t

186 alysis provides a paradigm for optics in the atomistic near-field.

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

188 Understanding the atomistic origin of defects in two-dimensional transitio

189 A key question in the field is what are the atomistic origins of this switching, i.e., what is diffe

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

191 logy's stories to be told in the language of atomistic physics.

192 For the first time, we reveal a detailed atomistic picture of long-time scale restructuring of Pd

193 usly been comprehensively understood from an atomistic point of view.

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

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

196 mained infeasible to simulate the folding of atomistic proteins at room temperature using conventiona

197 Atomistic reconstruction of signaling pathways in the Dn

198 ein model has been optimized with respect to atomistic reference simulations.

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

200 the structure of this protein and provide an atomistic representation of the full-length protein in t

201 s ad hoc back-mapping from coarse-grained to atomistic representations followed by spectral computati

202 proteins in general to provide interpretable atomistic representations of their otherwise elusive all

203 rare events in a rigorous manner, providing atomistic resolution over diffusive time scales using no

204 ach for l- and d-Lys over MFI zeolites at an atomistic resolution, the differential adsorption study

205 dna, that, in 30 min or less, can produce an atomistic-resolution structure of a self-assembled DNA n

206 se models, the first experimentally verified atomistic sandwich models of the LPP, will aid in the de

207 the occurrence of molecular dynamics at the atomistic scale in cocrystals, thereby displaying high p

208 In a new linkage, we connected atomistic scale information to protein, cell, and tissue

209 material are studied using well-established atomistic scale simulation techniques.

210 Atomistic scale simulations are used to calculate the in

211 Here, we employ static atomistic scale simulations to examine the defect proper

212 ween PQS and a model P. aeruginosa OM at the atomistic scale.

213 ted efforts in precision synthesis, advanced atomistic-scale in situ characterization, and comprehens

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

215 Using atomistic simulation based on the classical pair potenti

216 practical methods to extend the scale of the atomistic simulation by several orders of magnitude whil

217 In this review, we summarize the state of atomistic simulation methods for ion channels to underst

218 aces is one of the main challenges of modern atomistic simulation methods.

219 Furthermore, single-particle TEM imaging and atomistic simulation of reaction trajectories can inform

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

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

222 Here we use atomistic simulation to predict the efficacy of C12A7 to

223 e apply single-particle imaging coupled with atomistic simulation to study reaction pathways and rate

224 nmental transmission electron microscopy and atomistic simulation, we reveal that the cathode-water i

225 We are at a crossroads in atomistic simulation, where long time scale observation

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

227 Through atomistic simulations and biophysical, biochemical and c

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

229 Combining atomistic simulations and further mutagenesis experiment

230 Here atomistic simulations and machine learning methods are e

231 Combining atomistic simulations and machine learning techniques ca

232 In this work, both atomistic simulations and previous experimental data are

233 g these extensions in first principles-based atomistic simulations and the strategies being pursued t

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

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

236 Detailed atomistic simulations are constrained to shorter timesca

237 , how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG mo

238 Atomistic simulations can provide valuable, experimental

239 Atomistic simulations could complement experiments and s

240 Both in situ nanomechanical testing and atomistic simulations demonstrate that custom-designed l

241 Our microsecond-long atomistic simulations elucidate key structural differenc

242 Atomistic simulations further reveal that the excellent

243 In this work, atomistic simulations have been fully integrated with a

244 lop a multiscale approach combining numerous atomistic simulations in explicit solvent to construct M

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

246 However, atomistic simulations of phosphorus have remained an out

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

248 Analysis of transition paths in atomistic simulations of proteins shows that this coeffi

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

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

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

252 Additionally, atomistic simulations provide molecular insight into how

253 l membranes at the coarse-grained level, but atomistic simulations remain computationally challenging

254 Large-scale atomistic simulations reveal that this combination of be

255 Atomistic simulations revealed the dynamic appearance an

256 Using atomistic simulations spanning nearly 10 orders of magni

257 Both experimental investigations and atomistic simulations suggest that the cluster-cloud-med

258 from molecular-level modeling, particularly atomistic simulations that enhance understanding of pore

259 -based interatomic potentials give access to atomistic simulations that reach similar accuracy levels

260 ucture in a closed state, which was shown by atomistic simulations to be highly flexible in lipid bil

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

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

263 Therefore, we have performed atomistic simulations totaling 32.7 mus and cell-based i

264 Rather, based on our atomistic simulations we propose the theory that once in

265 We address these challenges by integrating atomistic simulations with high-resolution single-molecu

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

267 scale complexity cannot be fully captured by atomistic simulations, and the design of such materials

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

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

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

271 mplemented by cellular signalling assays and atomistic simulations, these structures reveal that extr

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

273 cular dynamics simulations validated against atomistic simulations, we explore the molecular mechanis

274 By using atomistic simulations, we investigate the orientation an

275 Using atomistic simulations, we reveal that the LCO of the mul

276 Using coarse-grained and atomistic simulations, we study various sequences of hom

277 olid-state NMR restraints with physics-based atomistic simulations.

278 e most effective way forward in the field of atomistic simulations.

279 mutagenesis experiments as well as detailed atomistic simulations.

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

281 antitative and validated through a series of atomistic simulations.

282 Here we have developed an atomistic spin model of elongated magnetite nanocrystals

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

284 To address these questions, we have employed atomistic stochastic Landau-Lifshitz-Gilbert simulations

285 y translate observed deuteration levels into atomistic structural information.

286 Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Bravehe

287 e inputs of a cryo-EM map, the corresponding atomistic structure, and the potential bilayer orientati

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

289 ticrossing model, parametrised directly from atomistic supercell calculations, quantitatively describ

290 ten not easily deducible from the underlying atomistic system.

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

292 Furthermore, it paves the way to atomistic understanding of interfacial reactions, at the

293 An atomistic understanding of metal transport in the human

294 These findings provide an atomistic understanding of non-volatile switching and op

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

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

297 ng available experimental data to provide an atomistic view of the interaction and dynamics of the cy

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

299 Although the variance among atomistic WE folding runs is significant, multiple indep

300 solution structure of human myeloma IgG2 by atomistic X-ray and neutron-scattering modeling.