A5014763956- Protein Structure and Dynamics
- Enzyme Structure and Function
- Mass Spectrometry Techniques and Applications
- stochastic dynamics and bifurcation
- Force Microscopy Techniques and Applications
- Spectroscopy and Quantum Chemical Studies
- Monoclonal and Polyclonal Antibodies Research
- RNA and protein synthesis mechanisms
- Scientific Research and Discoveries
- Nonlinear Dynamics and Pattern Formation
- Ecosystem dynamics and resilience
- Modeling, Simulation, and Optimization
- Advanced Chemical Physics Studies
- Computational Physics and Python Applications
- Polymer Surface Interaction Studies
- DNA and Nucleic Acid Chemistry
- Theoretical and Computational Physics
- Chemical Synthesis and Analysis
- Blood properties and coagulation
- Computational Drug Discovery Methods
- Photochemistry and Electron Transfer Studies
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- Diatoms and Algae Research
- Advanced Thermodynamics and Statistical Mechanics
Universitat Politècnica de Catalunya
2008-2023
Scuola Normale Superiore
2016-2017
University of Pisa
2016
Istituto Nanoscienze
2013
Institute for Research in Biomedicine
2006-2012
Barcelona Supercomputing Center
2008-2012
Universitat de Barcelona
2002-2009
Abstract Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, transient nature intermediates along transition pathways hampers their experimental detection, making underlying mechanisms elusive. Here we retrieve dynamic information on actual routes principal component analysis (PCA) structurally-rich ensembles and, in combination with coarse-grained simulations, explore landscapes five well-studied proteins. Modelling them as elastic...
FlexServ is a web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols coarse-grained determination dynamics using different versions Normal Mode Analysis (NMA), Brownian (BD) and Discrete Dynamics (DMD). It can also analyze user provided trajectories. allows complete flexibility large variety metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness collectivity measures, Lindemann's indexes, residue correlation,...
The analogue of temporal coherence resonance for spatial degrees freedom is reported. Specifically, we show that spatiotemporal noise able to optimally extract an intrinsic scale in nonlinear media close (but before) a pattern-forming instability. This effect observed model chemical reaction and the Swift-Hohenberg fluid convection. In latter case, phenomenon described analytically via approximate approach.
We discuss intrinsic noise effects in stochastic multiplicative-noise partial differential equations, which are qualitatively independent of the interpretation (Itô vs Stratonovich), particular context noise-induced ordering phase transitions. study a model which, contrary to all cases known so far, exhibits such transitions when is interpreted not only according Stratonovich, but also Itô. The main feature this absence linear instability at transition point. dynamical properties resulting...
The increasing number of nonsymbiotic plant hemoglobins discovered in genomic studies the past decade raises intriguing questions about their physiological role. Among them, hemoglobin AHb1 from Arabidopsis thaliana deserves particular attention, as it combines an extremely high oxygen affinity with internal hexacoordination distal histidine HisE7 to heme iron absence exogenous ligands. In order gain insight into structure-function relationships protein, ligand binding properties mutants two...
The Perturbed Matrix Method (PMM) approach to be used in combination with Molecular Dynamics (MD) trajectories (MD-PMM) has been recoded from scratch, improved several aspects, and implemented the Gaussian suite of programs for allowing a user-friendly yet flexible tool estimate quantum chemistry observables complex systems condensed phases. Particular attention devoted description rigid centers together powerful essential dynamics clustering approaches. default implementation is fully...
Abstract We present here a fast method for the exploration of channels in proteins based on molecular dynamics simulations probe particles discrete grid space defined by an ensemble protein conformations obtained either experimentally or out‐of‐the‐grid atomistic simulations. The is able to provide millisecond‐long trajectories with small computational effort, requires no human intervention defining possible exit pathways and can detect both major minor channels, giving correct balance...
We present a new method for fast molecular dynamics simulations in cases where the trajectories can be considered perturbation or combination of previously stored ones. The is designed postgenomic scenario, databases such as MoDEL will store curated equilibrium all biomolecules (proteins, nucleic acids, etc.) human interest. demonstrate that approach outlined here can, with accuracy and great computational efficiency, reproduce extend original trajectories, describe dynamical effects due to...
We present here the first application of a new algorithm, essential dynamics/molecular dynamics (ED/MD), to field small molecule docking. The method uses previously existing molecular (MD) ensemble protein or protein-drug complex generate, with very computational cost, perturbed ensembles which represent ligand-induced binding site flexibility in more accurate way than original trajectory. use these standard docking program leads superior performance same procedure using crystal structure...
Abstract Highly abundant proteins tend to evolve slowly (a trend called E-R anticorrelation), and a number of hypotheses have been proposed explain this phenomenon. The misfolding avoidance hypothesis attributes the anticorrelation abundance-dependent toxic effects protein misfolding. To avoid these effects, sequences (particularly those highly expressed proteins) would be under selection fold properly. One prediction is that should exhibit high thermostability (i.e., negative free energy...
Development of a novel Coarse-Grained (CG) model to study β<sub>2</sub>-microglobulin dynamical features related fibrillation: our one CG bead is able indicate propensities in the deformation behavior protein <italic>via</italic> investigation motion correlations.
First and second-order nonequilibrium phase transitions induced by an external nonlinear multiplicative noise are studied. A theoretical approach gives that the physical mechanism responsible for these is a instability of homogeneous phase. Mean–field analysis numerical simulations confirm prediction.
We present here a study of multiplicative-noise Stochastic Partial Differential Equations (SPDE) and their sensitivity to the stochastic interpretation (Ito or Stratonovich). analyze both static effects such as noise-induced phase transitions dynamical ones domain growth spatial structures in way towards steady state. discuss which circumstances particular choice induces qualitative changes.
External fluctuations can have counterintuitive ordering effects on a system. An example of these is the appearance nonequilibrium transition from disordered phase to an ordered one by increasing intensity external fluctuations. Nowadays two possible physical mechanisms responsible for noise‐induced transitions been observed: short time linear instability in sustained spatial coupling and new stable states effective potential. Our aim here present analytical numerical evidence nonlinear...