Graphics processing units in bioinformatics, computational biology and systems biology

MS Nobile, P Cazzaniga, A Tangherloni… - Briefings in …, 2017 - academic.oup.com
Abstract Several studies in Bioinformatics, Computational Biology and Systems Biology rely
on the definition of physico-chemical or mathematical models of biological systems at …

A perspective on the investigation of spectroscopy and kinetics of complex molecular systems with semiclassical approaches

R Conte, C Aieta, M Cazzaniga… - The Journal of Physical …, 2024 - ACS Publications
In this Perspective we show that semiclassical methods provide a rigorous hierarchical way
to study the vibrational spectroscopy and kinetics of complex molecular systems. The time …

Semiclassical “Divide-and-Conquer” method for spectroscopic calculations of high dimensional molecular systems

M Ceotto, G Di Liberto, R Conte - Physical Review Letters, 2017 - APS
A new semiclassical “divide-and-conquer” method is presented with the aim of
demonstrating that quantum dynamics simulations of high dimensional molecular systems …

On-the-fly ab initio semiclassical calculation of glycine vibrational spectrum

F Gabas, R Conte, M Ceotto - Journal of chemical theory and …, 2017 - ACS Publications
We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine,
calculated by Fourier transform of the wavepacket correlation function. It is based on a …

Integrated PK-PD and agent-based modeling in oncology

Z Wang, JD Butner, V Cristini, TS Deisboeck - Journal of pharmacokinetics …, 2015 - Springer
Mathematical modeling has become a valuable tool that strives to complement conventional
biomedical research modalities in order to predict experimental outcome, generate new …

“Divide and conquer” semiclassical molecular dynamics: A practical method for spectroscopic calculations of high dimensional molecular systems

G Di Liberto, R Conte, M Ceotto - The Journal of Chemical Physics, 2018 - pubs.aip.org
We extensively describe our recently established “divide-and-conquer” semiclassical
method [M. Ceotto, G. Di Liberto, and R. Conte, Phys. Rev. Lett. 119, 010401 (2017)] and …

Machine learning for vibrational spectroscopy via divide-and-conquer semiclassical initial value representation molecular dynamics with application to N …

M Gandolfi, A Rognoni, C Aieta, R Conte… - The Journal of Chemical …, 2020 - pubs.aip.org
A machine learning algorithm for partitioning the nuclear vibrational space into subspaces is
introduced. The subdivision criterion is based on Liouville's theorem, ie, the best …

“Divide-and-conquer” semiclassical molecular dynamics: An application to water clusters

G Di Liberto, R Conte, M Ceotto - The Journal of Chemical Physics, 2018 - pubs.aip.org
We present an investigation of vibrational features in water clusters performed by means of
our recently established divide-and-conquer semiclassical approach [M. Ceotto, G. Di …

Improved semiclassical dynamics through adiabatic switching trajectory sampling

R Conte, L Parma, C Aieta, A Rognoni… - The Journal of Chemical …, 2019 - pubs.aip.org
We introduce an improved semiclassical dynamics approach to quantum vibrational
spectroscopy. In this method, a harmonic-based phase space sampling is preliminarily …

Anharmonic vibrational eigenfunctions and infrared spectra from semiclassical molecular dynamics

M Micciarelli, R Conte, J Suarez… - The Journal of chemical …, 2018 - pubs.aip.org
We describe a new approach based on semiclassical molecular dynamics that allows
simulating infrared absorption or emission spectra of molecular systems with inclusion of …