1,320 research outputs found
Memristors for the Curious Outsiders
We present both an overview and a perspective of recent experimental advances
and proposed new approaches to performing computation using memristors. A
memristor is a 2-terminal passive component with a dynamic resistance depending
on an internal parameter. We provide an brief historical introduction, as well
as an overview over the physical mechanism that lead to memristive behavior.
This review is meant to guide nonpractitioners in the field of memristive
circuits and their connection to machine learning and neural computation.Comment: Perpective paper for MDPI Technologies; 43 page
The OpenMMPol Library for Polarizable QM/MM Calculations of Properties and Dynamics
We present a new library designed to provide a simple and straightforward way
to implement QM/AMOEBA and other polarizable QM/MM methods based on induced
point dipoles. The library, herein referred to as OpenMMPol, is free and
open-sourced and is engineered to address the increasing demand for accurate
and efficient QM/MM simulations. OpenMMPol is specifically designed to allow
polarizable QM/MM calculations of ground state energies and gradients, and
excitation properties. Key features of OpenMMPol include a modular architecture
facilitating extensibility, parallel computing capabilities for enhanced
performance on modern cluster architectures, and a user-friendly interface for
intuitive implementation and a simple and flexible structure for providing
input data. To show the capabilities of fered by the library we present an
interface with PySCF to perform QM/AMOEBA molecular dynamics, geometry
optimization and excited state calculation based on (TD)DFT
Towards Physarum Binary Adders
Plasmodium of \emph{Physarum polycephalum} is a single cell visible by
unaided eye. The plasmodium's foraging behaviour is interpreted in terms of
computation. Input data is a configuration of nutrients, result of computation
is a network of plasmodium's cytoplasmic tubes spanning sources of nutrients.
Tsuda et al (2004) experimentally demonstrated that basic logical gates can be
implemented in foraging behaviour of the plasmodium. We simplify the original
designs of the gates and show --- in computer models --- that the plasmodium is
capable for computation of two-input two-output gate and
three-input two-output . We assemble the
gates in a binary one-bit adder and demonstrate validity of the design using
computer simulation.Comment: Biosystems (2010), in press. Please download final version of the
paper from the Publishers's sit
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Development and analysis of Tinker-OpenMM as a GPU-based free energy perturbation engine
The utilization of computational technologies for the lead optimization process is one of the biggest challenges in the computational chemistry field. In this dissertation, I describe the addition of GPU-based absolute and relative free energy calculation methods using polarizable force field AMOEBA to Tinker-OpenMM. I then proceed to test the capabilities of this platform by studying the binding free energy and binding structures of derivatives of the MELK inhibitor IN17. Also, I present the implementation of virial-based pressure control to the Tinker-OpenMM platform that is needed for performing isobaric simulations.Cellular and Molecular Biolog
Tools for Biomolecular Modeling and Simulation
Electrostatic interactions play a pivotal role in understanding biomolecular systems, influencing their structural stability and functional dynamics. The Poisson-Boltzmann (PB) equation, a prevalent implicit solvent model that treats the solvent as a continuum while describes the mobile ions using the Boltzmann distribution, has become a standard tool for detailed investigations into biomolecular electrostatics. There are two primary methodologies: grid-based finite difference or finite element methods and body-fitted boundary element methods. This dissertation focuses on developing fast and accurate PB solvers, leveraging both methodologies, to meet diverse scientific needs and overcome various obstacles in the field
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