Publications related to In silico

Community-based reconstruction and simulation of a full-scale model of region CA1 of rat hippocampus

Henry Markram, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, James Gonzalo King, Lida Kanari, Ying Shi, Armando Romani, Davide Bella, Felix Schürmann, Werner Alfons Hilda Van Geit, Marwan Muhammad Ahmed Abdellah, Pramod Shivaji Kumbhar, Alexis Arnaudon, Jean-Denis Georges Emile Courcol, András Ecker, Juan Bautista Hernando Vieites, Michael Emiel Gevaert, Huanxiang Lu, Cyrille Pierre Henri Favreau, Michele Migliore, Vishal Sood, Liesbeth Maria L Vanherpe, Cristina Colangelo, Mohameth François Sy, Judit Planas Carbonell, Joni Henrikki Herttuainen, Genrich Ivaska, Anna-Kristin Kaufmann, Szabolcs Kali, Elvis Boci, Thomas Brice Delemontex, Carmen Alina Lupascu, Nadir Roman Guerrero, Rosanna Migliore, Alberto Antonietti, Fabien Petitjean, Julian Martin Budd, Juan Luis Riquelme Roman, , , , ,

Determination of Aortic Characteristic Impedance and Total Arterial Compliance From Regional Pulse Wave Velocities Using Machine Learning: An in-silico Study

Nikolaos Stergiopoulos, Vasiliki Bikia, Georgios Rovas, Stamatia Zoi Pagoulatou

In-vivo assessment of aortic characteristic impedance (Zao) and total arterial compliance (CT) has been hampered by the need for either invasive or inconvenient and expensive methods to access simultaneous recordings of aortic pressure and flow, wall thick ...

2021

Alpha-Synuclein oligomerization and aggregation: All models are useful but only if we know what they model This is the reply to a comment "Alpha-synuclein oligomerization and aggregation: A model will always be a model" on the original article "Monitoring alpha-synuclein oligomerization and aggregation using bimolecular fluorescence complementation assays: What you see is not always what you get". The articles are accompanied by a Preface "How good are cellular models?"

Hilal Lashuel

Alpha-synuclein oligomerization is one of the early events on the pathway to Lewy body formation. Therefore, interfering with this process holds tremendous potential for developing therapies that block alpha-Syn pathology formation and toxicity. The develo ...

Wiley-Blackwell2021

The Neurorobotic Platform: A simulation environment for brain-inspired robotics

Marc-Oliver Gewaltig, Paul Levi

The aim of the neurorobotic platform of the Human Brain Project is to offer scientists and technology developers a soft - ware and hardware infrastructure that allows them to connect pre-validated brain models to detailed simulations of ro- bot bodies and ...

VDE Verlag2016

Mechanics and co-evolution of allosteric materials and proteins

Riccardo Ravasio

The regulation of several processes inside and outside the cell depends on the action of a particular class of enzymes, called allosteric. In allosteric macromolecules, binding a ligand at one site affects the binding activity at a distal functional site, ...

EPFL2020

In Silico Discovery of Covalent Organic Frameworks for Carbon Capture

Berend Smit, Daniele Ongari, Christoph Leopold Talirz, Aliaksandr Yakutovich, Johanna Maria Huck, Kathryn Suzanne Deeg, Daiane Damasceno Borges, Nakul Rampal

We screen a database of more than 69 000 hypothetical covalent organic frameworks (COFs) for carbon capture using parasitic energy as a metric. To compute CO2-framework interactions in molecular simulations, we develop a genetic algorithm to tune the charg ...

2020

Computational characteristics and hardware implications of brain tissue simulations

Francesco Cremonesi

Understanding the link between the brain's anatomy and its function through computer simulations of neural tissue models is a widely used approach in computational neuroscience. This technique enables rapid prototyping and testing of hypotheses, allowing r ...

EPFL2019

A Process for Digitizing and Simulating Biologically Realistic Oligocellular Networks Demonstrated for the Neuro-Glio-Vascular Ensemble

Pierre Magistretti, Henry Markram, Felix Schürmann, Daniel Keller, Marwan Muhammad Ahmed Abdellah, Renaud Jolivet, Corrado Cali, Stefan Eilemann, Jay Coggan, Daniya Boges, Kalpana Kare, Markus Hadwiger, Marco Agus

One will not understand the brain without an integrated exploration of structure and function, these attributes being two sides of the same coin: together they form the currency of biological computation. Accordingly, biologically realistic models require ...

2018

An ecotoxicological view on neurotoxicity assessment

Wolfgang Schulz

The numbers of potential neurotoxicants in the environment are raising and pose a great risk for humans and the environment. Currently neurotoxicity assessment is mostly performed to predict and prevent harm to human populations. Despite all the efforts in ...

SPRINGEROPEN2018

In silico design and screening of hypothetical MOF-74 analogs and their experimental synthesis

Berend Smit, Kyriakos Stylianou, Samantha Lynn Anderson, Matthew David Witman

In this work we present the in silico design of metal-organic frameworks (MOFs) exhibiting 1-dimensional rod topologies. We introduce an algorithm for construction of this family of MOF topologies, and illustrate its application for enumerating MOF-74-type ...

2016

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

Sebastian Maerkl, Ekaterina Emilova Petrova, Bruno Emanuel Ferreira De Sousa Correia, Matthew Christopher Blackburn

The capability to rapidly design proteins with novel functions will have a significant impact on medicine, biotechnology and synthetic biology. Synthetic genes are becoming a commodity, but integrated approaches have yet to be developed that take full adva ...

Oxford Univ Press2016

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Julien Racle

Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus ...

EPFL2014

In Silico Design of Three-Dimensional Porous Covalent Organic Frameworks via Known Synthesis Routes and Commercially Available Species

Berend Smit, Cory Matthew Simon

Covalent organic frameworks (COFs) are a class of advanced nanoporous polymeric materials which combine the crystallinity of metalorganic frameworks (MOFs) with the stability and potentially low-cost organic chemistry of porous polymer networks (PPNs). Lik ...

Amer Chemical Soc2014

Cell Guidance on Nanogratings: A Computational Model of the Interplay between PC12 Growth Cones and Nanostructures

Silvestro Micera

Background: Recently, the effects of nanogratings have been investigated on PC12 with respect to cell polarity, neuronal differentiation, migration, maturation of focal adhesions and alignment of neurites. Methodology/Principal Findings: A synergistic proc ...

Public Library Science2013

Lack of Enantioselectivity in the SULT1A3-catalyzed Sulfoconjugation of Normetanephrine Enantiomers: An In Vitro and Computational Study

Sandrine Gerber, Jean-Baptiste Gualtierotti

(1R)-Normetanephrine is the natural stereoisomeric substrate for sulfotransferase 1A3 (SULT1A3)-catalyzed sulfonation. Nothing appears known on the enantioselectivity of the reaction despite its potential significance in the metabolism of adrenergic amines ...

Wiley-Blackwell2013

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold, Pablo Campomanes Ramos, Marilisa Neri, Stefano Vanni, Andrey Laktionov

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited sta ...

Schweizerische Chemische Gesellschaft2011

Emergent Properties of in silico Synaptic Transmission in a Model of the Rat Neocortical Column

Srikanth Ramaswamy

The cerebral cortex occupies nearly 80% of the entire volume of the mammalian brain and is thought to subserve higher cognitive functions like memory, attention and sensory perception. The neocortex is the newest part in the evolution of the cerebral corte ...

EPFL2011

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

Public Library of Science2011

Integration column: Microfluidic high-throughput screening

Sebastian Maerkl

Biology has always been a heavily technology limited field. Burgeoning fields such as systems biology require the development and implementation of new technologies, enabling high-throughput and high-fidelity measurements of large systems. Microfluidics pr ...

2009

Synchronous versus asynchronous modeling of gene regulatory networks

Giovanni De Micheli, Abhishek Garg, Ioannis Xenarios

In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, ...

2008