A5066453821- Protein Structure and Dynamics
- Lattice Boltzmann Simulation Studies
- Scientific Computing and Data Management
- Distributed and Parallel Computing Systems
- Computational Drug Discovery Methods
- Advanced Data Storage Technologies
- Material Dynamics and Properties
- Parallel Computing and Optimization Techniques
- Theoretical and Computational Physics
- Clay minerals and soil interactions
- Machine Learning in Materials Science
- Spectroscopy and Quantum Chemical Studies
- Advanced Thermodynamics and Statistical Mechanics
- Generative Adversarial Networks and Image Synthesis
- Fluid Dynamics and Turbulent Flows
- Layered Double Hydroxides Synthesis and Applications
- Monoclonal and Polyclonal Antibodies Research
- HIV Research and Treatment
- Quantum Computing Algorithms and Architecture
- Polymer Nanocomposites and Properties
- Nanopore and Nanochannel Transport Studies
- HIV/AIDS drug development and treatment
- RNA and protein synthesis mechanisms
- Quantum Information and Cryptography
- Mass Spectrometry Techniques and Applications
University College London
2016-2025
University of Amsterdam
2019-2025
Ludwig-Maximilians-Universität München
2024
Vrije Universiteit Amsterdam
2022
Transnational Press London
2019-2021
Brunel University of London
2020
Centrum Wiskunde & Informatica
2020
Poznan Supercomputing and Networking Center
2020
Yale University
2013-2019
University of London
2014-2018
We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. use programmable array of superconducting qubits to compute energy surface molecular hydrogen using two distinct algorithms. First, we experimentally execute unitary coupled cluster method variational eigensolver. Our efficient implementation predicts correct dissociation within chemical accuracy numerically exact result. Second, demonstrate canonical algorithm...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMonte Carlo Molecular Modeling Studies of Hydrated Li-, Na-, and K-Smectites: Understanding the Role Potassium as a Clay Swelling InhibitorE. S. Boek, P. V. Coveney, N. T. SkipperCite this: J. Am. Chem. Soc. 1995, 117, 50, 12608–12617Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/ja00155a025https://doi.org/10.1021/ja00155a025research-articleACS...
Patterning of functional blood vessel networks is achieved by pruning superfluous connections. The cellular and molecular principles regression are poorly understood. Here we show that mediated dynamic polarized migration endothelial cells, representing anastomosis in reverse. Establishing analyzing the first axial polarity map all cells a remodeling vascular network, propose balanced movement maintains primitive plexus under low shear conditions metastable state. We predict flow-induced...
For the computational design of new polymeric materials, accurate methods for determining glass transition temperature (Tg) are required. We apply an ensemble approach in molecular dynamics (MD) and examine its predictions Tg their associated uncertainty. separate uncertainty into aleatoric contributions arising from dynamical chaos that due to scenarios chosen compute Tg. propose a scenario computing Tg, where density–temperature behavior is computed by running all temperatures...
The rheological properties of colloidal suspensions spheres, rods, and disks have been studied using a mesoscopic simulation technique, known as dissipative particle dynamics (DPD). In DPD, suspension is modeled system large particles in liquid interacting point particles. For the calculation hydrodynamic interactions, this method computationally more efficient than conventional techniques continuum model for solvent. Applying steady-shear rate to particulate suspensions, we measured...
This comprehensive work investigates: the role of computers in understanding complexity; spontaneous emergence order universe; how nature can solve problems that traditionally defeat scientists; and likelihood intelligence will evolve within computers.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Modeling of Clay Hydration: A Study Hysteresis Loops in the Swelling Curves Sodium MontmorillonitesE. S. Boek, P. V. Coveney, and N. T. SkipperCite this: Langmuir 1995, 11, 12, 4629–4631Publication Date (Print):December 1, 1995Publication History Published online1 May 2002Published inissue 1 December 1995https://pubs.acs.org/doi/10.1021/la00012a008https://doi.org/10.1021/la00012a008research-articleACS PublicationsRequest reuse...
The aim of hybrid methods in simulations is to communicate regions with disparate time and length scales. Here, a fluid described at the atomistic level within an inner region P coupled outer C by continuum dynamics. matching both descriptions matter made across overlapping and, general, consists two-way coupling scheme (C-->P P-->C) that conveys mass, momentum, energy fluxes. contribution hereby presented twofold. First, it treats unsteady flows more importantly, handles exchange between...
European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now nearly 2 years. The VPH network of excellence (NoE) is helping development common standards, open-source software, freely accessible data and model repositories, various training dissemination activities project. It also to coordinate many clinically targeted projects that have funded FP7 calls. An initial vision was defined by 6 strategy a physiome (STEP) 2006. time assess...
Large-scale atomistic simulations, which we define as containing more than 100 000 atoms, are becoming commonplace computational resources increase and efficient classical molecular dynamics algorithms developed. With the advent of grid-computing methods, it is now possible to simulate even larger systems efficiently. Using this new technology, have simulated montmorillonite clay up approximately ten million atoms whose dimensions approach those a realistic platelet. This considerably...
To explain drug resistance by computer simulations at the molecular level, we first have to assess accuracy of theoretical predictions. Herein report an application mechanics Poisson−Boltzmann surface area (MM/PBSA) technique ranking binding affinities inhibitor saquinavir with wild type (WT) and three resistant mutants HIV-1 protease: L90M, G48V, G48V/L90M. For each ligand−protein complex 10 ns fully unrestrained dynamics (MD) explicit solvent. We investigate convergence, internal...
Endothelial cells respond to molecular and physical forces in development vascular homeostasis. Deregulation of endothelial responses flow-induced shear is believed contribute many aspects cardiovascular diseases including atherosclerosis. However, how signals shear-mediated integrate regulate patterning poorly understood. Here we show that non-canonical Wnt signalling regulates sensitivity forces. Loss Wnt5a/Wnt11 renders more sensitive shear, resulting axial polarization migration against...
The use of molecular simulation to estimate the strength macromolecular binding free energies is becoming increasingly widespread, with goals ranging from lead optimization and enrichment in drug discovery personalizing or stratifying treatment regimes. In order realize potential such approaches predict new results, not merely explain previous experimental findings, it necessary that methods used are reliable accurate, their limitations thoroughly understood. However, computational cost...
We show, via three-dimensional immersed-boundary-finite-element-lattice-Boltzmann simulations, that deformability-based red blood cell (RBC) separation in deterministic lateral displacement (DLD) devices is possible. This due to the deformability-dependent extension of RBCs and enables us predict a priori which will be displaced given DLD geometry. Several diseases affect deformability human cells. Malaria-infected or sickle cells, for example, tend become stiffer than their healthy...
The presentation of potentially pathogenic peptides by major histocompatibility complex (MHC) molecules is one the most important processes in adaptive immune defense. Prediction peptide-MHC (pMHC) binding affinities therefore a principal objective theoretical immunology. Machine learning techniques achieve good results if substantial experimental training data are available. Approaches based on structural information become necessary sufficiently similar unavailable for specific MHC allele,...
Abstract Graphite's lubricating properties due to the “weak” interactions between individual layers have long been known. However, these are not weak enough allow graphite readily exfoliate into graphene on a large scale. Separating down single sheet is an intense area of research as scientists attempt utilize graphene's superlative properties. The exfoliation and processing layered materials governed by friction layers. Friction macroscale can be intuitively understood, but there little...
The accurate prediction of the binding affinities ligands to proteins is a major goal in drug discovery and personalized medicine. time taken make such predictions similar importance their accuracy, precision, reliability. In past few years, an ensemble based molecular dynamics approach has been proposed that provides route reliable free energies on mechanics Poisson–Boltzmann surface area method which meets requirements speed, Here, we describe equivalent methodology thermodynamic...
Controlling the structure of graphene and oxide (GO) phases is vitally important for any its widespread intended applications: highly ordered arrangements nanoparticles are needed thin-film or membrane applications GO, dispersed composite materials, 3D porous hydrogels. By combining coarse-grained molecular dynamics newly developed accurate models driving forces that lead to various morphologies resolved. Two hydrophilic polymers, poly(ethylene glycol) (PEG) poly(vinyl alcohol) (PVA), used...