Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models
Sign Up to like & getrecommendations! Published in 2018 at "Biophysical Journal"
DOI: 10.1016/j.bpj.2017.11.012
Abstract: The importance of charge-charge interactions in the thermal stability of proteins is widely known. pH and ionic strength play a crucial role in these electrostatic interactions, as well as in the arrangement of ionizable residues… read more here.
Keywords: protein; grained models; coarse grained; salt concentration ... See more keywords
Comparison of two coarse-grained models of cis-polyisoprene with and without pressure correction
Sign Up to like & getrecommendations! Published in 2017 at "Polymer"
DOI: 10.1016/j.polymer.2017.09.062
Abstract: Abstract We investigate two coarse-grained models of a cis -polyisoprene melt. The bonded interactions which are used in both models are derived by Boltzmann inversion of the probability distributions of the bonded variables in a… read more here.
Keywords: grained models; two coarse; coarse grained; pressure correction ... See more keywords
How Does the Surface Tension Depend on the Surface Area with Coarse-Grained Models?
Sign Up to like & getrecommendations! Published in 2018 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.8b00158
Abstract: We propose to investigate the size-effects on the surface tension calculated with coarse-grained (CG) models. We investigate different liquid-vapor (LV) and liquid-liquid (LL) interfaces with the MARTINI force field and original CG models designed for… read more here.
Keywords: surface area; surface; grained models; coarse grained ... See more keywords
Development of Coarse-Grained Models for Polymers by Trajectory Matching
Sign Up to like & getrecommendations! Published in 2019 at "ACS Omega"
DOI: 10.1021/acsomega.9b00144
Abstract: Coarse-grained (CG) models allow for simulating the necessary time and length scales relevant to polymers. However, developing realistic force fields at the CG level is still a challenge because there is no guarantee that the… read more here.
Keywords: development coarse; grained models; model; coarse grained ... See more keywords
Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction
Sign Up to like & getrecommendations! Published in 2020 at "Green Chemistry"
DOI: 10.1039/d0gc01823f
Abstract: Ionic liquids (ILs) are remarkable green solvents, which find applications in many areas of nano- and biotechnology including extraction and purification of value-added compounds or fine chemicals. These liquid salts possess versatile solvation properties that… read more here.
Keywords: extraction; liquid; grained models; models imidazolium ... See more keywords
Calculation of therapeutic antibody viscosity with coarse-grained models, hydrodynamic calculations and machine learning-based parameters
Sign Up to like & getrecommendations! Published in 2021 at "mAbs"
DOI: 10.1080/19420862.2021.1907882
Abstract: ABSTRACT High viscosity presents a challenge for manufacturing and drug delivery of therapeutic antibodies. The viscosity is determined by protein–protein interactions among many antibodies. Molecular simulation is a promising method to study protein–protein interactions; however,… read more here.
Keywords: viscosity; antibody; grained models; coarse grained ... See more keywords
Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates
Sign Up to like & getrecommendations! Published in 2024 at "PLOS Computational Biology"
DOI: 10.1101/2024.08.28.610132
Abstract: Intracellular liquid–liquid phase separation (LLPS) of proteins and nucleic acids is a fundamental mechanism by which cells compartmentalize their components and perform essential biological functions. Molecular simulations play a crucial role in providing microscopic insights… read more here.
Keywords: coarse grained; residue resolution; protein; resolution ... See more keywords
Predicting Throughput of Distributed Stochastic Gradient Descent
Sign Up to like & getrecommendations! Published in 2022 at "IEEE Transactions on Parallel and Distributed Systems"
DOI: 10.1109/tpds.2022.3151739
Abstract: Training jobs of deep neural networks (DNNs) can be accelerated through distributed variants of stochastic gradient descent (SGD), where multiple nodes process training examples and exchange updates. The total throughput of the nodes depends not… read more here.
Keywords: stochastic gradient; grained models; gradient descent; throughput distributed ... See more keywords
Benchmarking coarse-grained models of organic semiconductors via deep backmapping
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Chemistry"
DOI: 10.3389/fchem.2022.982757
Abstract: The potential of mean force is an effective coarse-grained potential, which is often approximated by pairwise potentials. While the approximated potential reproduces certain distributions of the reference all-atom model with remarkable accuracy, important cross-correlations are… read more here.
Keywords: benchmarking coarse; coarse; models organic; force ... See more keywords
Applications of Coarse-Grained Models in Metabolic Engineering
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Molecular Biosciences"
DOI: 10.3389/fmolb.2022.806213
Abstract: Mathematical modeling is a promising tool for better understanding of cellular processes. In recent years, the development of coarse-grained models has gained attraction since these simple models are able to capture and describe a broad… read more here.
Keywords: metabolic engineering; models metabolic; production; applications coarse ... See more keywords
Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications
Sign Up to like & getrecommendations! Published in 2019 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms20153774
Abstract: Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to… read more here.
Keywords: biomolecules applications; grained models; advances coarse; recent advances ... See more keywords