ライフサイエンスコーパス: coarse-grain

1 r molecular dynamics simulations, RACER (RnA CoarsE-gRained).

2 markedly reduced for this ensemble type with coarse graining.

3 In both approaches, we deliberately coarse-grain a new clickstream proprietary dataset to pr

4 illance data, which are far sparser and more coarse-grained, achieve only 56% sensitivity.

5 A coarse-grained alumina could also reach a translucency l

6 coupled to yellow and consistent crumb, with coarse grain and well-perceivable sour taste and odor.

7 l strategies with variable discretization or coarse graining and unbinding dynamics, and although gen

8 nal approaches-statistical mechanical model, coarse-grained and all-atom MD simulations-reveal that t

9 ne interactions and function, we carried out coarse-grained and all-atom molecular dynamics simulatio

10 Here, we used a combination of coarse-grained and all-atom molecular dynamics simulatio

11 In both coarse-grained and all-atom molecular dynamics simulatio

12 combine molecular simulations based on both coarse-grained and atomistic models with coevolutionary

13 Using coarse-grained and atomistic simulations, we study vario

14 uantitative scoring approaches, however, are coarse-grained and lack precise neuroanatomic localizati

15 and electrical properties compared to their coarse-grained and nanograined counterparts.

16 n protocol which decreases the resolution by coarse-graining and averaging over short similarity dist

17 based multiscale simulations where a dynamic coarse-graining and force-blending method is required.

18 NA-vWF interaction by integrating atomistic, coarse-grained, and Brownian dynamics simulations, with

19 time-dependent multidimensional data with a coarse-grained approach and map key dynamical features w

20 complementary roles that both atomistic and coarse-grained approaches play in such simulations.

21 use a silent lip-read signal to synthesize a coarse-grained auditory speech representation in early a

22 To this end, we developed a coarse-grained bead-and-spring model and investigated it

23 inverse Brownian dynamics method based on a coarse-grained bead-spring chain model has been proposed

24 ations (or in silico experiments) of generic coarse-grained bead-spring polymer chains in an implicit

25 protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of tr

26 static or dynamic selection of atoms or even coarse-grained beads for the density calculation.

27 overlapping, variable-length segments (i.e., coarse-grained beads) for each component protein sequenc

28 ract mechanical parameters for inputs into a coarse-grained biophysical polymer model that successful

29 The framework consists of a coarse-grained but mechanistic description of host physi

30 Furthermore, we discuss how organizational coarse-graining can be applied to spatial dynamics by sh

31 obably all quasibrittle materials, including coarse-grained ceramics, rocks, stiff foams, fiber compo

32 This approach uses the Martini coarse grain (CG) model to describe the receptors, lipid

33 (48 J/cm(2)) is almost comparable to that of coarse grained (CG) Cu: 55 J/cm(2).

34 In this study, we performed coarse grained (CG) molecule dynamics (MD) simulations o

35 Coarse-grain (CG) molecular dynamics simulations are emp

36 ongoing development of a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion.

37 Our previous work used a coarse-grained (CG) model to simulate the action of F(0)

38 Here, we introduce a set of machine-learned coarse-grained (CG) models (ML-BOP, ML-BOP(dih), and ML-

39 sentations that correspond to particle-based coarse-grained (CG) models for a simple microscopic mode

40 Here, we present a coarse-grained (CG) simulation method that enables micro

41 Coarse-grained (CG) simulations of ESCRT assembly at HIV

42 A coarse-grain computational method integrates biophysical

43 We use a coarse-grained computational model to capture nanotube l

44 Here, we develop a minimal coarse-grained computational model to identify the physi

45 er adhesion assembly, we therefore develop a coarse-grained computational model.

46 Our results are gained from coarse-grained computer simulations and first-principles

47 Here, we use coarse-grained computer simulations and the theory of as

48 rstanding recently revealed by atomistic and coarse-grained computer simulations of nanoscale process

49 of principle, we apply torsional forces to a coarse-grained continuum model of the antibody protein i

50 h a high loading (10 kg/m(2) ) of relatively coarse-grained crushed basalt significantly increased th

51 size and complexity, but here we argue that coarse-grained data introduce errors that, in biological

52 Specifically, we formulate a coarse-grained description of cell polarity through self

53 Our model, which is based on a coarse-grained description of ligands and solvent effect

54 mics simulations with combined atomistic and coarse-grained description of NPs reveal the emergence o

55 In this work, we pursue a coarse-grained description of these systems by proposing

56 er demonstrates the capability of the "quasi-coarse-grained dynamics" (QCGD) simulation method to unr

57 roduce a filament-based simulation model for coarse-grained, effective motor-mediated interaction bet

58 For this purpose, we utilize coarse-grained elastic network models.

59 ore slowly than the generation time (i.e., a coarse-grained environment) a population will not experi

60 tead, we propose that adaptive plasticity in coarse-grained environments evolves as a by-product of i

61 Deriving such coarse-grained equations is notoriously difficult and of

62 greater room-temperature strength than their coarse-grained equivalents, in part owing to a large red

63 ndeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular con

64 Retraining for different coarse-graining factors shows the parameterization perfo

65 ow that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal

66 We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanop

67 mulate model lipid bilayers with the MARTINI coarse-grained force field on length scales of tens of n

68 e dedicated equipment or limit themselves to coarse-grained force measurements on the micron scale.

69 ural interpolation for the construction of a coarse-grained free energy landscape.

70 improved radiation tolerance comparing with coarse-grained, fully dense Au.

71 as a proxy for toxicity, enzyme sharing, and coarse-grained functional similarity.

72 ph sampling protocol to construct and sample coarse-grained graph representations of RNAs from a give

73 fiber model, which couples fine-grained and coarse-grained HbS fiber models through a mesoscopic ada

74 beta(3), we developed a modified form of the coarse-grained heterogeneous elastic network model (hENM

75 In this study, we used a combination of coarse graining, hierarchical natural move Monte Carlo a

76 Based on a predictive coarse-grained IDP model, we identified a region of the

77 The coarse-grain iron content of exponentially growing cells

78 Using coarse-grained kinetic Langevin dynamics, we performed c

79 We employed coarse-grained Langevin dynamics simulations to monitor

80 We are able to relate each more coarse-grained level to a finer one, which allows us to

81 d phase separation in model membranes at the coarse-grained level, but atomistic simulations remain c

82 More generally, the aim is the extraction of coarse-grained, macroscopic information from stochastic

83 Pegmatites are shallow, coarse-grained magmatic intrusions with crystals occasio

84 SpringSaLaD models biomolecules in a coarse-grained manner as a group of linked spherical sit

85 features to train the models in a simple and coarse-grained manner.

86 Here, we have extended the coarse-grain Martini force field to include RNA after ou

87 In this work, a combination of coarse-grained "Martini" and all-atom simulations are us

88 Wear rates in the initially soft (coarse grained) material were shown to be remarkably low

89 Here we construct and analyze a coarse-grained mathematical model of the fission yeast r

90 To this end, we performed coarse-grain MD simulations of the Photosystem II comple

91 utations, providing parameters for improving coarse-grained MD accuracy and speed, and many others.

92 Coarse-grained MD reveals that the lipids reorganize loc

93 Using a combination of all-atom and coarse-grained MD simulations and sequence covariation a

94 ed or unfolded, and were directly taken from coarse-grained MD simulations.

95 monstrate the orchestration of various novel coarse-graining methods by applying them to the mitotic

96 ar systems can greatly benefit from a set of coarse-graining methods that, ideally, can be automatica

97 we have employed the elastic folder model, a coarse-grained, minimalistic representation of the polyp

98 ned with simulations based on a transferable coarse-grained model allows us to predict accurately the

99 ariables for mechanical deformations using a coarse-grained model and then sampling along these defor

100 tative agreement with the predictions of our coarse-grained model as well as qualitative agreement wi

101 to deal with a complex system is to build a coarse-grained model capable of catching its main physic

102 Here, we have used a coarse-grained model describing the relation between obs

103 Molecular dynamics simulations using a coarse-grained model enables estimation of free-energy l

104 We use an accurate coarse-grained model for DNA and stochastic molecular dy

105 n Dry Martini, an efficient implicit solvent coarse-grained model for lipids, and the Lattice Boltzma

106 ic generalization of a previously introduced coarse-grained model for stabilization of proteins by su

107 Using a unique coarse-grained model for the power stroke of a single MV

108 ics simulations and a previously established coarse-grained model having each residue represented by

109 We used a simple whole-cell coarse-grained model of cell physiology that combines th

110 Using a coarse-grained model of DNA and lac repressor (LacI) in

111 We use a coarse-grained model of DNA to study the kinetics and th

112 ing in EMT and drug resistance, we analyze a coarse-grained model of phenotypic switching between two

113 rowth laws are discussed in the context of a coarse-grained model of phototrophic growth and availabl

114 A coarse-grained model of SUHI coupled with a stochastic s

115 We use molecular simulations by creating a coarse-grained model of the MT-kinesin complex, which re

116 roximately 8 degrees ) using a residue-level coarse-grained model of the ribosome.

117 erimental observations using a parameterized coarse-grained model of VWF.

118 s somewhat counterintuitive idea in a simple coarse-grained model results in the prediction that ther

119 Recently, Brownian dynamics simulations of a coarse-grained model system reproduced protracted pausin

120 Using a minimal coarse-grained model that allows us to simulate thousand

121 We generate a bottom-up coarse-grained model that demonstrates similar membrane-

122 Here, we introduce a coarse-grained model that enables simulation of networks

123 rform molecular dynamics simulations using a coarse-grained model that includes a 1/r(4) potential fo

124 We introduce a coarse-grained model that links population, background c

125 timescales of fusion, we developed a highly coarse-grained model that retains key biophysical SNARE

126 Our study used homology modeling and a coarse-grained model to generate all of the possible "en

127 We use the oxDNA coarse-grained model to provide a detailed characterizat

128 We present a new coarse-grained model to realistically simulate the bindi

129 We developed a mesoscale coarse-grained model to study the characteristics of tra

130 Here, we develop a coarse-grained model to systematically explore the effec

131 Here, we use a coarse-grained model to systematically study how variati

132 The coarse-grained model we consider is that of Ginzburg-Lan

133 We develop a coarse-grained model which connects statistical features

134 We use our coarse-grained model with a set of secondary structural

135 rded as the simplest and most representative coarse-grained model, has been widely adopted to analyze

136 We have applied a structure-based coarse-grained model, with an explicit Debye-Huckel char

137 sely matching the level of resolution of the coarse-grained model.

138 possibilities for future improvements of the coarse-grained model.

139 nd demonstrated by computer simulations of a coarse-grained model.

140 such as proteins and protein complexes with coarse-grained modeling and simulations.

141 Alternative coarse-grained modeling must also incorporate appropriat

142 Coarse-grained modeling of conjugated polymers has becom

143 e DNA/RNA nanostructures simulated using the coarse-grained modeling tool, oxDNA, which has grown in

144 We performed systematic coarse-grained modeling using an elastic network model a

145 ons of these assemblies include all-atom and coarse-grained modeling, but modeling their conformation

146 Here we show atomistic, coarse-grained modelling combined with advanced simulati

147 Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling

148 Further, experiments and coarse-grained modelling showed the substrate alone freq

149 affinity of calcium (Ca(2+)) by integrating coarse-grained models and all-atomistic simulations with

150 folded proteins using atomistic simulations, coarse-grained models and analytic theory.

151 ordant with theoretical predictions based on coarse-grained models and inferences drawn from single-m

152 Coarse-grained models are compared with 3D cryo-electron

153 hesis, and most conventional structure-based coarse-grained models do not allow for nonnative structu

154 Inevitably, such coarse-grained models introduce a set of phenomenologica

155 dy and analysis, construction of atomic from coarse-grained models is required.

156 to study the crystallization of a family of coarse-grained models of chiral molecules with a broad r

157 model to be broadly applicable and useful in coarse-grained models of gas transport in metals.

158 as proven to be a valuable tool to determine coarse-grained models of membrane-embedded Bcl-2 protein

159 In this work, we study coarse-grained models of organic glass formers containin

160 More specifically, we developed two coarse-grained models of proteins, which interact identi

161 Both FD-AFM and computational studies on coarse-grained models of rhodopsin revealed that the act

162 l implementations entail compromises between coarse-grained models of the spin label that lower the r

163 ows the assessment of the limitations of the coarse-grained models proposed.

164 Coarse-grained models represent attractive approaches to

165 nding, we derived a series of topology-based coarse-grained models that mimicked various ACTR mutants

166 ting from these strategies have been used in coarse-grained models to predict light-dependent growth

167 tematic experiments and simulations based on coarse-grained models to show that the collective intera

168 Consequently, it can produce most economical coarse-grained models while faithfully preserving the sh

169 Importantly, these coarse-grained models, while only calibrated based on bi

170 edure is general and can be adapted to other coarse-grained models.

171 nslation that are difficult to study in more coarse-grained models.

172 To answer this question, we developed a coarse-grain molecular dynamics model for the axon that

173 mines its overall stiffness, we introduced a coarse-grain molecular dynamics model of the axon membra

174 Coarse-grain molecular dynamics simulations are a key to

175 Coarse-grain molecular dynamics simulations reveal that

176 and cholesterol clustering by cav-1 by using coarse-grain molecular dynamics simulations.

177 Here, we use coarse-grained molecular dynamics (MD) simulation and su

178 Results of coarse-grained Molecular Dynamics (MD) simulations of no

179 mensional structure folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations

180 By combining coarse-grained molecular dynamics and newly developed ac

181 By using a multiscale coarse-grained molecular dynamics approach, we show that

182 We present OpenRBC, a coarse-grained molecular dynamics code, which is capable

183 R toxicity, a one-bead-per-amino-acid (1BPA) coarse-grained molecular dynamics model is used to study

184 t a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master

185 First, a computational modeling approach by coarse-grained molecular dynamics simulation of the whol

186 Using native mass spectrometry, coarse-grained molecular dynamics simulations and functi

187 Coarse-grained molecular dynamics simulations are applie

188 mammalian cell membranes, we have performed coarse-grained molecular dynamics simulations containing

189 Consistent with this possibility, extensive coarse-grained molecular dynamics simulations of a BR tr

190 We present coarse-grained molecular dynamics simulations of monomer

191 Here, we report the results of coarse-grained molecular dynamics simulations of monomer

192 Coarse-grained molecular dynamics simulations of the HTL

193 Indeed, initial coarse-grained molecular dynamics simulations of the lon

194 Coarse-grained molecular dynamics simulations of the str

195 Coarse-grained molecular dynamics simulations reveal tha

196 Here, we use high-throughput coarse-grained molecular dynamics simulations to charact

197 We used coarse-grained molecular dynamics simulations to charact

198 In this work, we use coarse-grained molecular dynamics simulations to elucida

199 Here, we use atomistic and coarse-grained molecular dynamics simulations to investi

200 Here we use coarse-grained molecular dynamics simulations to investi

201 Here, using coarse-grained molecular dynamics simulations validated

202 A combination of coarse-grained molecular dynamics simulations, Laurdan m

203 bined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are ab

204 Using coarse-grained molecular dynamics simulations, we explor

205 d-state NMR spectroscopy in combination with coarse-grained molecular dynamics simulations, we report

206 With atomistic and coarse-grained molecular dynamics simulations, we resolv

207 Using coarse-grained molecular dynamics simulations, we show t

208 esence of MG2a and L18W-PGLa to all-atom and coarse-grained molecular dynamics simulations.

209 terized from nearly 200 mus of residue-based coarse-grained molecular dynamics simulations.

210 The combination of coarse-grained molecular dynamics studies and NMR should

211 In this work, using coarse-grained molecular dynamics, the transmembrane dom

212 hate (PIP2) -containing lipid bilayer, using coarse-grained molecular dynamics.

213 g the new technique are analyzed by means of coarse-grained molecular simulations and experimentally

214 Here, using coarse-grained molecular simulations and statistical mec

215 to the binding of multiple chaperones using coarse-grained molecular simulations.

216 ian-Langevin dynamics principles to derive a coarse-graining multiscale myofilament model that can de

217 Coarse-grained network modeling demonstrated that an abr

218 ial tradeoffs associated with the process of coarse graining NMMII ensembles and highlight the robust

219 We employ both coarse-grained node dropout and fine-grained edge dropou

220 In particular, coarse-grained node dropout can efficiently and systemat

221 -screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motio

222 semble through a Monte Carlo simulation of a coarse-grained nucleosome model with sequence-dependent

223 Coarse graining of these ensemble types from two sets of

224 his functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological ni

225 n is progressively decreased by hierarchical coarse-graining of the anatomical regions.

226 r beds typically have an "armoured" layer of coarse grains on the surface, which acts to protect fine

227 ndom forest to learn a parameterization from coarse-grained output of a three-dimensional high-resolu

228 gene expression(1-3), but these measurements coarse-grain over the individual copies of the gene, whe

229 Using a coarse-grained particle-network model, we first establis

230 a Voronoi partitioning of the point cloud of coarse-grained particles, and is continuously updated ov

231 ach to simultaneously capture both fine- and coarse-grain patterns of variability.

232 5) The model provides a coarse-grained phenomenological description of diffusion

233 We show that all primary, coarse-grained platy calcitic lateral walls are covered

234 identify the heterogenous dynamics of model coarse-grained polymer chains both in 'bulk' and near th

235 Using coarse-grained polymer theory and numerical simulations,

236 Here, we present a coarse-grained polynucleotide model developed to fill th

237 spectral data as input in the refinement of coarse-grained potentials.

238 rge problems, we also develop an approximate coarse-graining procedure that avoids the need for negat

239 to improve model elaboration, refinement and coarse graining procedures to better understand the rele

240 We use coarse grained protein conformational search, efficient

241 etric binding energies for each state of the coarse-grained protein corresponding to the symmetry of

242 bly of single nucleosomes using a predictive coarse-grained protein DNA model with transferable force

243 del underlying the server's predictions is a coarse-grained protein force field which has its roots i

244 In this work, a predictive coarse-grained protein force field, the associative memo

245 Using a predictive coarse-grained protein force field, we compute and compa

246 The coarse-grained protein model has been optimized with res

247 Here, using a coarse-grained protein model, molecular dynamics (MD) si

248 lations suggest an emergent length scale for coarse-graining proteins, as well as a qualitative disti

249 approach, expanding the recently established coarse-grained proteome allocation models from steady-st

250 e the level of sensitivity of spectra to the coarse-grained representation back-mapping protocol.

251 ams for multicomponent systems comprising of coarse-grained representations of multivalent proteins.

252 spectra of conjugated polymers directly from coarse-grained representations while avoiding repetitive

253 The only recourse is to use approximate coarse-grained representations, which aim to accurately

254 ures, we have developed an open software for coarse-grained RNA folding simulations, guided by human

255 We introduce a coarse-grained RNA model for molecular dynamics simulati

256 Coarse-grained rules are widely used in chemistry, physi

257 f the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of w

258 viding strong evidence for the prediction of coarse-grained semantic features that goes beyond the pr

259 ubules, with diameters of about 30 nm, carry coarse-grained Shannon information to the centrosome adj

260 Here, we use coarse-grain simulation to study three scenarios, all re

261 escribe the development and application of a coarse-grained simulation approach that addresses these

262 e integration efficiencies, obtained using a coarse-grained simulation approach, robustly predicted e

263 Unlike most coarse-grained simulation approaches, the higher-level o

264 ationally demanding than fully atomistic and coarse-grained simulation methodologies; however, it has

265 We present a coarse-grained simulation model that is capable of simul

266 Using a coarse-grained simulation model, we rationalized that th

267 We review atomistic and coarse-grained simulation studies of amyloid peptides in

268 uctures of single domains, based on previous coarse-grained simulation studies.

269 We use a coarse-grained simulation that takes into account the di

270 Here, we use theoretical modeling and coarse-grained simulation to explore the interplay betwe

271 -molecule force-spectroscopy experiments and coarse-grained simulation.

272 A folding, and demonstrates the potential of coarse-grained simulations as a tool for rationally tuni

273 Coarse-grained simulations confirm the experimentally ob

274 lecular modeling using atomic resolution and coarse-grained simulations corroborates our experimental

275 Coarse-grained simulations employing native centric mode

276 Although the MARTINI coarse-grained simulations give the correct free energy

277 Coarse-grained simulations of a wide range of junction t

278 certainty by demonstrating the capability of coarse-grained simulations of membrane protein insertion

279 wer these questions in the affirmative using coarse-grained simulations of the self-organized polymer

280 ted in the covalent network was predicted by coarse-grained simulations of the system's chemical stru

281 All-atom and coarse-grained simulations reproduced some of the experi

282 Combining theory and coarse-grained simulations shows that the DNA sequence a

283 ational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis

284 physical parameters for this process and use coarse-grained simulations with explicit cross-linkers t

285 Using elasticity theory and coarse-grained simulations, we analyze the conditions re

286 e these results to those obtained by MARTINI coarse-grained simulations.

287 ng approach, combining a previously reported coarse-grained small-scale proteome allocation model wit

288 Here, we present a simple, coarse-grained statistical model of niche construction c

289 Our coarse-grained structural model thus suggests that the h

290 (ii) an efficient approach for FRET-assisted coarse-grained structural modeling, and all-atom molecul

291 echanism of domain swapping of M(pro)C using coarse-grained structure-based models and molecular dyna

292 terials, a rigorous bridge between simulated coarse-grained structures and spectroscopy has not been

293 mechanics, allowed better contractility with coarse graining, though connectivity was still markedly

294 s of Azoarcus ribozyme, based on an accurate coarse-grained three-site interaction model with explici

295 in difficulties by applying a gradient-based coarse graining to RNA-ligand systems and solving the pr

296 procedures such as ad hoc back-mapping from coarse-grained to atomistic representations followed by

297 RAG uses coarse-grained tree graphs to represent RNA secondary st

298 le microstructural damage in single-crystal, coarse-grained, ultrafine-grained and nanograined metals

299 nct minima of a Ginzburg-Landau functional-a coarse-grained version of the elastic energy, which pena

300 Coarse-grained volcanic ash leads to significantly highe