Dynamical memristors for higher-complexity neuromorphic computing

S Kumar, X Wang, JP Strachan, Y Yang… - Nature Reviews …, 2022 - nature.com
Research on electronic devices and materials is currently driven by both the slowing down
of transistor scaling and the exponential growth of computing needs, which make present …

A survey of biodiversity informatics: Concepts, practices, and challenges

LMR Gadelha Jr, PC de Siracusa… - … : Data Mining and …, 2021 - Wiley Online Library
The unprecedented size of the human population, along with its associated economic
activities, has an ever‐increasing impact on global environments. Across the world …

Molecular origins of force-dependent protein complex stabilization during bacterial infections

MCR Melo, DEB Gomes… - Journal of the American …, 2022 - ACS Publications
The unbinding pathway of a protein complex can vary significantly depending on
biochemical and mechanical factors. Under mechanical stress, a complex may dissociate …

Heterogeneous CPU+ GPU-enabled simulations for DFTB molecular dynamics of large chemical and biological systems

SI Allec, Y Sun, J Sun, CA Chang… - Journal of chemical …, 2019 - ACS Publications
We introduce a new heterogeneous CPU+ GPU-enhanced DFTB approach for the routine
and efficient simulation of large chemical and biological systems. Compared to …

SEEKR2: Versatile multiscale milestoning utilizing the OpenMM molecular dynamics engine

LW Votapka, AM Stokely, AA Ojha… - Journal of chemical …, 2022 - ACS Publications
We present SEEKR2 (simulation-enabled estimation of kinetic rates version 2)─ the latest
iteration in the family of SEEKR programs for using multiscale simulation methods to …

Predicting ligand binding kinetics using a Markovian milestoning with voronoi tessellations multiscale approach

BR Jagger, AA Ojha, RE Amaro - Journal of Chemical Theory and …, 2020 - ACS Publications
Accurate and efficient computational predictions of ligand binding kinetics can be useful to
inform drug discovery campaigns, particularly in the screening and lead optimization …

Multiscale simulation approaches to modeling drug–protein binding

BR Jagger, SE Kochanek, S Haldar, RE Amaro… - Current opinion in …, 2020 - Elsevier
Highlights•Drug binding is inherently multiscale as it occurs over a broad range of length
and time scales.•Multiscale simulation methods combine molecular descriptions to access …

Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike

MCR Melo, RC Bernardi - Biophysical Journal, 2023 - cell.com
Over a century ago, physicists started broadly relying on theoretical models to guide new
experiments. Soon thereafter, chemists began doing the same. Now, biological research …

Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites

DK Sarkar, B Surpeta, J Brezovsky - Journal of Chemical Theory …, 2024 - ACS Publications
Because most proteins have buried active sites, protein tunnels or channels play a crucial
role in the transport of small molecules into buried cavities for enzymatic catalysis. Tunnels …

Field programmable gate arrays for enhancing the speed and energy efficiency of quantum dynamics simulations

JM Rodrı́guez-Borbón, A Kalantar… - Journal of chemical …, 2020 - ACS Publications
We present the first application of field programmable gate arrays (FPGAs) as new,
customizable hardware architectures for carrying out fast and energy-efficient quantum …