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pro vyhledávání: '"Chen, Yaoyi"'
Machine-learned coarse-grained (MLCG) molecular dynamics is a promising option for modeling biomolecules. However, MLCG models currently require large amounts of data from reference atomistic molecular dynamics or substantial computation for training
Externí odkaz:
http://arxiv.org/abs/2407.01286
Autor:
Charron, Nicholas E., Musil, Felix, Guljas, Andrea, Chen, Yaoyi, Bonneau, Klara, Pasos-Trejo, Aldo S., Venturin, Jacopo, Gusew, Daria, Zaporozhets, Iryna, Krämer, Andreas, Templeton, Clark, Kelkar, Atharva, Durumeric, Aleksander E. P., Olsson, Simon, Pérez, Adrià, Majewski, Maciej, Husic, Brooke E., Patel, Ankit, De Fabritiis, Gianni, Noé, Frank, Clementi, Cecilia
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with simil
Externí odkaz:
http://arxiv.org/abs/2310.18278
Autor:
Krämer, Andreas, Durumeric, Aleksander P., Charron, Nicholas E., Chen, Yaoyi, Clementi, Cecilia, Noé, Frank
Machine-learned coarse-grained (CG) models have the potential for simulating large molecular complexes beyond what is possible with atomistic molecular dynamics. However, training accurate CG models remains a challenge. A widely used methodology for
Externí odkaz:
http://arxiv.org/abs/2302.07071
Publikováno v:
J. Chem. Theory Comput. 2023, XXXX, XXX, XXX-XXX
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular processes on time- and length-scales inaccessible to all-atom simulations. Parameterizing CG force fields to match all-atom simulations has mainly relied on forc
Externí odkaz:
http://arxiv.org/abs/2203.11167
Autor:
Que, Jianyu, Chen, Sijing, Chan, Ngan Yin, Wu, Suying, Zhang, Li, Chen, Yaoyi, Liu, Jingrou, Chen, Mingxuan, Chen, Lixia, Li, Shirley Xin, Lin, Duoduo, Liu, Farong, Wing, Yun Kwok
Publikováno v:
In Sleep Medicine June 2024 118:81-87
Autor:
Chen, Yaoyi, Krämer, Andreas, Charron, Nicholas E., Husic, Brooke E., Clementi, Cecilia, Noé, Frank
Publikováno v:
J. Chem. Phys. 155, 084101 (2021)
Accurate modeling of the solvent environment for biological molecules is crucial for computational biology and drug design. A popular approach to achieve long simulation time scales for large system sizes is to incorporate the effect of the solvent i
Externí odkaz:
http://arxiv.org/abs/2106.07492
Autor:
Husic, Brooke E., Charron, Nicholas E., Lemm, Dominik, Wang, Jiang, Pérez, Adrià, Majewski, Maciej, Krämer, Andreas, Chen, Yaoyi, Olsson, Simon, de Fabritiis, Gianni, Noé, Frank, Clementi, Cecilia
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it are consi
Externí odkaz:
http://arxiv.org/abs/2007.11412
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Publikováno v:
In South African Journal of Botany July 2023 158:90-97
Autor:
Durumeric, Aleksander E.P., Charron, Nicholas E., Templeton, Clark, Musil, Félix, Bonneau, Klara, Pasos-Trejo, Aldo S., Chen, Yaoyi, Kelkar, Atharva, Noé, Frank, Clementi, Cecilia
Publikováno v:
In Current Opinion in Structural Biology April 2023 79