T
+34 946 567 842
F
+34 946 567 842
E
eakhmatskaya@bcamath.org
Information of interest
Other links
Profile at Ikerbasque Berkeley Lab QMMMy major research interest is in the development of numerical methods for modelling and simulation of complex systems. The main features of my research career have been: Work on the interface of Mathematics, Biology, Chemistry, Physics, Computational Statistics and Computer Science
Broad diapason of research activities from developing theoretical methods and implementing them on high performance, computers to application of software codes for study of important phenomena and processes.
Collaboration with multi-international academic and industrial partners (Oxford University (UK), Imperial College London (UK), St Andrews University (UK), Berkeley Labs (USA), Accelrys Inc. (USA), NAG (UK), POLYMAT (Spain), energiGUNE (Spain), bioGUNE (Spain) among others).
Work experience:
- Academic: Cornell University, USA; University of Manchester, Imperial College, UK.
- Industrial: Fujitsu Centre for Information Technology, UK. Fujitsu Laboratories of Europe, UK.
-
A macroscopic clock model to solve the paradox of Schrödinger’s cat
(2024-12-01)We propose detecting the moment an atom emits a photon by means of a nearly classical macroscopic clock and discuss its viability. It is shown that what happens in such a measurement depends on the relation between the ...
-
Imaginary past of a quantum particle moving on imaginary time
(2024-05-21)The analytical continuation of classical equations of motion to complex times suggests that a tunneling particle spends in the barrier an imaginary duration 𝑖|\mathcal{T}|. Does this mean that it takes a finite time to ...
-
Adaptive multi-stage integration schemes for Hamiltonian Monte Carlo
(2024-01-26)Hamiltonian Monte Carlo (HMC) is a powerful tool for Bayesian statistical inference due to its potential to rapidly explore high dimensional state space, avoiding the random walk behavior typical of many Markov Chain Monte ...
-
A data-mining approach to understanding the impact of multi-doping on the ionic transport mechanism of solid electrolytes materials: the case of dual-doped Ga<inf>0.15</inf>/Sc<inf>y</inf> Li<inf>7</inf>La<inf>3</inf>Zr<inf>2</inf>O<inf>12</inf>
(2024-01-19)This study presents novel computational methods applied to the technologically significant solid electrolyte materials, Li6.55+yGa0.15La3Zr2−yScyO12 (Ga0.15/Scy-LLZO), in order to investigate the effect of the distribution ...
-
The crystal chemistry and reactivity of ternary Na2Fe3Cl8 from the NaCl-FeCl2 system and its potential application as coating layer for cathode in sodium ion batteries
(2023-12-15)This report explores theoretical and experimental methods to characterize the ternary phases arising from the NaCl + FeCl2 system at both low (150 °C) and high temperatures (550 °C), through milling and evaporation processing ...
-
BayFlux: A Bayesian Method to Quantify Metabolic Fluxes and their Uncertainty at the Genome Scale.
(2023-11-10)Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13C Metabolic Flux Analysis (13C MFA) is considered to ...
-
A Novel Mathematical Approach for Analysis of Integrated Cell–Patient Data Uncovers a 6-Gene Signature Linked to Endocrine Therapy Resistance
(2023-11-09)A significant number of breast cancers develop resistance to hormone therapy. This progression, while posing a major clinical challenge, is difficult to predict. Despite important contributions made by cell models and ...
-
Anion Trapping and Ionic Conductivity Enhancement in PEO-Based Composite Polymer-Li<inf>7</inf>La<inf>3</inf>Zr<inf>2</inf>O<inf>12</inf> Electrolytes: The Role of the Garnet Li Molar Content
(2023-06-13)The successful development of all-solid-state batteries will provide solutions for many problems facing current Li-ion batteries, such as high flammability, limited energy density, poor cyclability and low cation transference ...
-
Reducing Model Complexity by Means of the Optimal Scaling: Population Balance Model for Latex Particles Morphology Formation.
(2023-04-15)Rational computer-aided design of multiphase polymer materials is vital for rapid progress in many important applications, such as: diagnostic tests, drug delivery, coatings , additives for constructing materials, cosmetics, ...
-
A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism
(2023)Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 ...
-
On the interfacial lithium dynamics in Li7La3Zr2O12:poly(ethylene oxide) (LiTFSI) composite polymer-ceramic solid electrolytes under strong polymer phase confinement
(2022-05-27)A better molecular-level understanding of Li+ diffusion through ceramic/polymer interfaces is key to designing high-performance composite solid-state electrolytes for all-solid-state batteries. By considering as a case ...
-
Numerical Regge pole analysis of resonance structures in state-to-state reactive differential cross sections
(2022-04-19)This is the third (and the last) code in a collection of three programs [Sokolovski et al. (2011), Akhmatskaya et al. (2014)] dedicated to the analysis of numerical data, obtained in an accurate simulation of an atom-diatom ...
-
Wigner's friends, tunnelling times and Feynman's "only mystery of quantum mechanics"
(2022-01-13)Recent developments in elementary quantum mechanics have seen a number of extraordinary claims regarding quantum behaviour, and even questioning internal consistency of the theory. These are, we argue, different disguises ...
-
Unveiling Interfacial Li-Ion Dynamics in Li7La3Zr2O12/PEO(LiTFSI) Composite Polymer-Ceramic Solid Electrolytes for All-Solid-State Lithium Batteries
(2021-06-23)Unlocking the full potential of solid-state electrolytes (SSEs) is key to enabling safer and more-energy dense technologies than today’s Li-ion batteries. In particular, composite materials comprising a conductive, flexible ...
-
Tunnelling times, Larmor clock, and the elephant in the room
(2021-05-11)A controversy surrounding the “tunnelling time problem” stems from the seeming inability of quantum mechanics to provide, in the usual way, a definition of the duration a particle is supposed to spend in a given region of ...
-
Multiscale Modelling and Simulation of Advanced Battery Materials
(2021)Development of efficient strategies for the rational design of materials involved in the production and storage of renewable energy is essential for accelerating the transition to a low-carbon economy. To contribute to ...
-
An optimal scaling to computationally tractable dimensionless models: Study of latex particles morphology formation
(2020-02)In modelling of chemical, physical or biological systems it may occur that the coefficients, multiplying various terms in the equation of interest, differ greatly in magnitude, if a particular system of units is used. Such ...
-
Exploring Li-ion conductivity in cubic, tetragonal and mixed-phase Al-substituted Li7La3Zr2O12 using atomistic simulations and effective medium theory
(2019-08-15)Garnet Li7La3Zr2O12 (LLZO) is a promising solid electrolyte candidate for solid-state Li-ion batteries, but at room temperature it crystallizes in a poorly Li-ion conductive tetragonal phase. To this end, partial substitution ...
-
Modified Hamiltonian Monte Carlo for Bayesian Inference
(2019-07-22)The Hamiltonian Monte Carlo (HMC) method has been recognized as a powerful sampling tool in computational statistics. We show that performance of HMC can be significantly improved by incorporating importance sampling and ...
-
No Time at the End of the Tunnel
(2018-08-21)Modern atto-second experiments seek to provide an insight into a long standing question: “how much time does a tunnelling particle spend in the barrier?” Traditionally, quantum theory relates this duration to the delay ...
-
Multi-stage splitting integrators for sampling with modified Hamiltonian Monte Carlo methods
(2018-07-17)Modified Hamiltonian Monte Carlo (MHMC) methods combine the ideas behind two popular sampling approaches: Hamiltonian Monte Carlo (HMC) and importance sampling. As in the HMC case, the bulk of the computational cost of ...
-
Revealing the Mechanism of Sodium Diffusion in NaxFePO4 Using an Improved Force Field
(2018-04-02)Olivine NaFePO4 is a promising cathode material for Na-ion batteries. Intermediate phases such as Na0.66FePO4 govern phase stability during intercalation-deintercalation processes, yet little is known about Na+ diffusion ...
-
Atomistic Insight into Ion Transport and Conductivity in Ga/Al-Substituted Li$_7$La$_3$Zr$_2$O$_{12}$ Solid Electrolytes
(2018-01-09)Garnet-structured Li$_{7}$La$_{3}$Zr$_{2}$O$_{12}$ is a promising solid electrolyte for next-generation solid-state Li batteries. However, sufficiently fast Li-ion mobility required for battery applications only emerges ...
-
An even simpler understanding of quantum weak values
(2018-01)We explain the properties and clarify the meaning of quantum weak values using only the basic notions of elementary quantum mechanics.
-
Adaptive Splitting Integrators for Enhancing Sampling Efficiency of Modified Hamiltonian Monte Carlo Methods in Molecular Simulation
(2017-10-24)The modified Hamiltonian Monte Carlo (MHMC) methods, i.e., importance sampling methods that use modified Hamiltonians within a Hybrid Monte Carlo (HMC) framework, often outperform in sampling efficiency standard techniques ...
-
Reexamination of continuous fuzzy measurement on two-level systems
(2017-04-10)Imposing restrictions on the Feynman paths of the monitored system has in the past been proposed as a universal model-free approach to continuous quantum measurements. Here we revisit this proposition and demonstrate that ...
-
Enhancing sampling in atomistic simulations of solid state materials for batteries: a focus on olivine NaFePO$_4$
(2017-03-07)The study of ion transport in electrochemically active materials for energy storage systems requires simulations on quantum-, atomistic- and meso-scales. The methods accessing these scales not only have to be effective but ...
-
Assessment of van der Waals inclusive density functional theory methods for layered electroactive materials
(2017-01-01)Computational-driven materials discovery requires efficient and accurate methods. Density functional theory (DFT) meets these two requirements for many classes of materials. However, DFT-based methods have limitations. One ...
-
Adaptive multi-stage integrators for optimal energy conservation in molecular simulations
(2016-10-01)We introduce a new Adaptive Integration Approach (AIA) to be used in a wide range of molecular simulations. Given a simulation problem and a step size, the method automatically chooses the optimal scheme out of an available ...
-
Numerical simulation of extreme wave runup during storm events in Tramandaí Beach, Rio Grande do Sul, Brazil
(2015-12-31)We present a high resolution analysis of the interaction of irregular waves with natural and urban structures leading to extreme wave runup. Horizontal runup data, instantaneous flooding maps, and wave propagation beyond ...
-
Relative frequencies of constrained events in stochastic processes: An analytical approach
(2015-12-31)The stochastic simulation algorithm (SSA) and the corresponding Monte Carlo (MC) method are among the most common approaches for studying stochastic processes. They relies on knowledge of interevent probability density ...
-
Complex angular momentum theory of state-to-state integral cross sections: Resonance effects in the $F + HD \to HF(v' = 3) + D$ reaction
(2015-12-31)State-to-state reactive integral cross sections (ICSs) are often affected by quantum mechanical resonances, especially near a reactive threshold. An ICS is usually obtained by summing partial waves at a given value of ...
-
Non-Markovian models of the growth of a polymer chain
(2015-12-31)Using simple exactly solvable models, we show that event-dependent time delays may lead to significant non-Poisson effects in the statistics of polymer chain growth. The results are confirmed by stochastic simulation of ...
-
Multiple-time-stepping generalized hybrid Monte Carlo methods
(2014-12-31)Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [2-4], molecular dynamics and hybrid Monte Carlo, can be further improved ...
-
Constant pressure hybrid Monte Carlo simulations in GROMACS
(2014-12-31)Adaptation and implementation of the Generalized Shadow Hybrid Monte Carlo (GSHMC) method for molecular simulation at constant pressure in the NPT ensemble are discussed. The resulting method, termed NPT-GSHMC, combines ...
-
Impact of competitive processes on controlled radical polymerization
(2014-12-31)The kinetics of radical polymerization have been systematically studied for nearly a century and in general are well understood. However, in light of recent developments in controlled radical polymerization many kinetic ...
-
Computer software for understanding resonances and resonance-related phenomena in chemical reactions
(2014-12-31)In numerical modelling of chemical reactions one calculates the scattering matrix for the required values of energy and angular momentum. Having done so, one still faces the non-trivial task of extracting detailed information ...
-
Numerical Regge pole analysis of resonance structures in elastic, inelastic and reactive state-to-state integral cross sections
(2014-12-31)We present a detailed description of a FORTRAN code for evaluation of the resonance contribution a Regge trajectory makes to the integral state-to-state cross section (ICS) within a specified range of energies. The ...
-
'Superluminal paradox' in wave packet propagation and its quantum mechanical resolution
(2013-12-31)We analyse in detail the reshaping mechanism leading to apparently 'superluminal' advancement of a wave packet traversing a classically forbidden region. In the coordinate representation, a barrier is shown to act as an ...
-
Interference mechanism of seemingly superluminal tunneling
(2013-12-31)Apparently "superluminal" transmission, e.g., in quantum tunneling and its variants, occurs via a subtle interference mechanism which allows reconstruction of the entire spatial shape of a wave packet from its front tail. ...
-
Dynamic modeling of the morphology of multiphase waterborne polymer particles
(2013-12-31)Multiphase waterborne polymer particles provide advantages in more demanding applications, and their performance depends on particle morphology. Currently, no dynamic model for the prediction of the development of the ...
-
Combining stochastic and deterministic approaches within high efficiency molecular simulations
(2013-12-31)Generalized Shadow Hybrid Monte Carlo (GSHMC) is a method for molecular simulations that rigorously alternates Monte Carlo sampling from a canonical ensemble with integration of trajectories using Molecular Dynamics (MD). ...
-
Particle Morphology
(2013-12-31)This chapter discusses the morphology of latex particles obtained mainly by (mini)emulsion polymerisation. It describes some applications of these particles, and discusses the factors that influence the particle morphology. ...
-
Molecular dynamics simulations of iron- and aluminum-loaded serum transferrin: Protonation of tyr188 is necessary to prompt metal release
(2012-12-31)Serum transferrin (sTf) carries iron in blood serum and delivers it into cells by receptor-mediated endocytosis. The protein can also bind other metals, including aluminum. The crystal structures of the metal-free and ...
-
Dynamic modeling of the morphology of latex particles with in situ formation of graft copolymer
(2012-12-31)Modification of the polymer-polymer interfacial tension is a way to tailor-make particle morphology of waterborne polymer-polymer hybrids. This allows achieving a broader spectrum of application properties and maximizing ...
-
Multiscale simulations of the antimicrobial peptide maculatin 1.1: Water permeation through disordered aggregates
(2012-12-31)The antimicrobial peptide maculatin 1.1 (M1.1) is an amphipathic α-helix that permeabilizes lipid bilayers. In coarse-grained molecular dynamics (CG MD) simulations, M1.1 has previously been shown to form membrane-spanning ...
-
Causality, 'superluminality', and reshaping in undersized waveguides
(2012-12-31)We analyse the reshaping mechanism leading to apparently 'superluminal' advancement of a pulse traversing an undersized section of a waveguide. For frequencies below the first inelastic threshold (cut off one), there are ...
-
Classification of resonance Regge trajectories and a modified Mulholland formula
(2011-12-31)We employ a simple potential model to analyze the effects which a Regge trajectory, correlating with a bound or a metastable state at zero angular momentum, has on an integral cross section. A straightforward modification ...
-
Extracting S-matrix poles for resonances from numerical scattering data: Type-II Padé reconstruction
(2011-12-31)We present a FORTRAN 77 code for evaluation of resonance pole positions and residues of a numerical scattering matrix element in the complex energy (CE) as well as in the complex angular momentum (CAM) planes. Analytical ...
-
Hartman effect and weak measurements that are not really weak
(2011-12-31)We show that in wave packet tunneling, localization of the transmitted particle amounts to a quantum measurement of the delay it experiences in the barrier. With no external degree of freedom involved, the envelope of the ...
-
Meso-GSHMC: A stochastic algorithm for meso-scale constant temperature simulations
(2011-12-31)We consider the problem of time-stepping/sampling for molecular and meso-scale particle dynamics. The aim of the work is to derive numerical time-stepping methods that generate samples exactly from the desired target ...
Numerical Regge pole analysis of resonance structures in state-to-state reactive differential cross sections (DCS_Regge)
This is the third (and the last) code in a collection of three programs [Sokolovski et al. (2011), Akhmatskaya et al. (2014)] dedicated to the analysis of numerical data, obtained in an accurate simulation of an atom-diatom chemical reaction. Our purpose is to provide a detailed complex angular momentum (CAM) analysis of the resonance effects in reactive angular scattering. The code evaluates the contributions of a Regge trajectory (or trajectories) to a differential cross section in a specified range of energies. The contribution is computed with the help of the methods described in [Dobbyn et al. (1999), Sokolovski and Msezane (2004), Sokolovski et al. (2007)]. Regge pole positions and residues are obtained by analytically continuing S-matrix element, calculated numerically for the physical integer values of the total angular momentum, into the complex angular momentum plane using the PADE_II program [Sokolovski et al. (2011)]. The code represents a reactive scattering amplitude as a sum of the components corresponding to a rapid “direct” exchange of the atom, and the various scenarios in which the reactants form long-lived intermediate complexes, able to complete several rotations before breaking up into products.
Authors: Elena Akhmatskaya
License: the CPC non-profit use license agreement - Mendeley Data
Numerical Regge pole analysis of resonance structures in elastic, inelastic and reactive state-to-state integral cross sections (ICS_Regge)
ICS_Regge is a suite of FORTRAN codes for evaluation of the resonance contribution a Regge trajectory makes to the integral state-to-state cross section (ICS) within a specified range of energies. The contribution is evaluated with the help of the Mulholland formula (Macek et al., 2004) and its variants (Sokolovski et al., 2007; Sokolovski and Akhmatskaya, 2011). Regge pole positions and residues are obtained by analytically continuing S-matrix element, evaluated numerically for the physical values of the total angular momentum, into the complex angular momentum plane using the PADE_II program (Sokolovski et al., 2011). The code decomposes an elastic, inelastic, or reactive ICS into a structured, resonance, and a smooth, ‘direct’, components, and attributes observed resonance structure to resonance Regge trajectories.
Authors: Elena Akhmatskaya
License: the CPC non-profit use license agreement - Mendeley Data
Extracting S-matrix poles for resonances from numerical scattering data: type-II Padé reconstruction(PADE II)
The code is designed for evaluation of resonance pole positions and residues of a numerical scattering matrix element in the complex energy (CE) as well as in the complex angular momentum (CAM) planes. Analytical continuation of the S-matrix element is performed by constructing a type-II Pade approximant from given physical values. The algorithm involves iterative ‘preconditioning’ of the numerical data by extracting its rapidly oscillating potential phase component. The code has the capability of adding non-analytical noise to the numerical data in order to select ‘true’ physical poles, investigate their stability and evaluate the accuracy of the reconstruction. It has an option of employing multiple-precision (MPFUN) package developed by D.H. Bailey wherever double precision calculations fail due to a large number of input partial waves (energies) involved.
Authors: Elena Akhmatskaya
License: the CPC non-profit use license agreement - Mendeley Data
Date | Title | Number | Author/s | Status |
---|---|---|---|---|
2013-11-19 | A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System | 8589127 | E. V. Akhmatskaya, S. Reich | |
2013-08-13 | A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System Using Shadow Hamiltonians | 8510084 | E. V. Akhmatskaya, S. Reich | |
2013-05-28 | Method, Apparatus and Computer Program for Simulating Behaviour of Thermodynamic Systems | US 8452576 | S. Reich, E. V. Akhmatskaya, R. H. Nobes | |
2011-03-05 | Method, Apparatus and Computer Program for Molecular Simulation | US007908129 | E. V. Akhmatskaya, R. H. Nobes, S. Reich | |
2011-01-12 | A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System | EP2273395 (A1) | E. V. Akhmatskaya, S. Reich | Published |
2011-01-12 | A Method, Apparatus and Computer Program for Multiple Time Stepping Simulation of a Thermodynamic System Using Shadow Hamiltonians | EP2273396 (A1) | E. V. Akhmatskaya, S. Reich | Published |
2010-02-03 | Method, Apparatus and Computer Program for Simulating Behaviour of Thermodynamic Systems | GB 2462261 A | S. Reich, E. V. Akhmatskaya, R. H. Nobes | Published |
2009-02-11 | Method, Apparatus and Computer Program for Molecular Simulation | GB 2451701 A | E. V. Akhmatskaya, S. Reich, R. H. Nobes | Published |
|
- An Introduction to Monte Carlo methods: Extensions, Variations and Applications of Monte Carlo Method - BCAM & UPV/EHU Courses 2012-2013 (BCAM)
- Workshop on Dynamical Systems and Applications, Bilbao, Basque Country - Member of Scientific Committee - 10-11-December, 2013
- 9th American Institute of Mathematical Sciences International Conference on Dynamical Systems and Differential Equations (AIMS 2012), Orlando, USA - Special Session Organizer - 1-5 July, 2012
- Mini-symposium on Non-linear dynamics applied to biological modelling, Bilbao, Basque Country - Member of Organizing Committee - 09 February, 2012
- The Second HPC-GA Workshop, Bilbao, Basque Country - Member of Organizing Committee - 11-15 March, 2013
- Quantum Days in Bilbao IV: Mathematical Methods in Atomic and Molecular Physics, Bilbao, Spain - Organizer - 15-16 July, 2014
- 10th American Institute of Mathematical Sciences Conference on Dynamical Systems, Differential Equations and Applications (AIMS 2014), Madrid, Spain - Special Session Organizer - 07-11 July, 2014
- The International Conference on Scientific Computation and Differential Equations, SciCADE 2015, Enhanced Sampling Methods, Minisymposium, Potsdam, Germany - Special Session Organizer - 14-18 September, 2015
- Quantum Days in Bilbao V: Mathematical Methods in Atomic and Molecular Physics - Satellite of QRS XIII, Bilbao, Spain - Organizer - 13-14 July, 2015
- BCAM - IMUVA Summer School on Uncertainty Quantification for Applied Problems, Bilbao, Basque Country, Spain - Organizer - 4-7 July, 2016
- 131st European Study Group with Industry (ESGI), Bilbao, Basque Country, Spain - Member of Scientific Committee - 15-19 May, 2017
- Mini-symposium "Advances in Modelling Multiscale Systems and their Applications", the VIII International Conference on Coupled Problems in Science and Engineering, Coupled 2019, Sitges, Spain - Organizer - 3 June, 2019 - 5 August, 2019
- International Summer School on Fractional and Other Nonlocal Models, Bilbao, Basque Country, Spain - Organizer - 28-31 May, 2018
- 150th European Study Group with Industry (ESGI), Bilbao, Basque Country, Spain - Member of Scientific Committee - 21-25 October, 2019