Autonomous discovery in the chemical sciences part II: outlook

CW Coley, NS Eyke, KF Jensen - … Chemie International Edition, 2020 - Wiley Online Library
This two‐part Review examines how automation has contributed to different aspects of
discovery in the chemical sciences. In this second part, we reflect on a selection of …

Accelerators for classical molecular dynamics simulations of biomolecules

D Jones, JE Allen, Y Yang… - Journal of chemical …, 2022 - ACS Publications
Atomistic Molecular Dynamics (MD) simulations provide researchers the ability to model
biomolecular structures such as proteins and their interactions with drug-like small …

[HTML][HTML] Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

S Páll, A Zhmurov, P Bauer, M Abraham… - The Journal of …, 2020 - pubs.aip.org
The introduction of accelerator devices such as graphics processing units (GPUs) has had
profound impact on molecular dynamics simulations and has enabled order-of-magnitude …

Anton 3: twenty microseconds of molecular dynamics simulation before lunch

DE Shaw, PJ Adams, A Azaria, JA Bank… - Proceedings of the …, 2021 - dl.acm.org
Anton 3 is the newest member in a family of supercomputers specially designed for atomic-
level simulation of molecules relevant to biology (eg, DNA, proteins, and drug molecules) …

86 PFLOPS deep potential molecular dynamics simulation of 100 million atoms with ab initio accuracy

D Lu, H Wang, M Chen, L Lin, R Car, E Weinan… - Computer Physics …, 2021 - Elsevier
We present the GPU version of DeePMD-kit, which, upon training a deep neural network
model using ab initio data, can drive extremely large-scale molecular dynamics (MD) …

FASDA: An FPGA-aided, scalable and distributed accelerator for range-limited molecular dynamics

C Wu, T Geng, A Guo, S Bandara, P Haghi… - Proceedings of the …, 2023 - dl.acm.org
Conducting long-timescale simulations of small molecules using Molecular Dynamics (MD)
is crucial in drug design. However, traditional methods to accelerate the process, including …

High-speed and low-power molecular dynamics processing unit (MDPU) with ab initio accuracy

P Mo, Y Zhang, Z Zhao, H Sun, J Li, D Guan… - npj Computational …, 2024 - nature.com
Molecular dynamics (MD) is an indispensable atomistic-scale computational tool widely-
used in various disciplines. In the past decades, nearly all ab initio MD and machine …

FPDeep: Scalable acceleration of CNN training on deeply-pipelined FPGA clusters

T Wang, T Geng, A Li, X **… - IEEE Transactions on …, 2020 - ieeexplore.ieee.org
Deep convolutional Neural Networks (CNNs) have revolutionized numerous applications,
but the demand for ever more performance remains unabated. Scaling CNN computations to …

Quantum-based molecular dynamics simulations using tensor cores

J Finkelstein, JS Smith, SM Mniszewski… - Journal of Chemical …, 2021 - ACS Publications
Tensor cores, along with tensor processing units, represent a new form of hardware
acceleration specifically designed for deep neural network calculations in artificial …

Long-Range MD Electrostatics Force Computation on FPGAs

S Bandara, A Ducimo, C Wu… - IEEE Transactions on …, 2024 - ieeexplore.ieee.org
Strong scaling of long-range electrostatic force computation, which is a central concern of
long timescale molecular dynamics simulations, is challenging for CPUs and GPUs due to …